Starting phenix.real_space_refine
on Sun Aug 24 19:55:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8du4_27715/08_2025/8du4_27715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8du4_27715/08_2025/8du4_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_27715/08_2025/8du4_27715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8du4_27715/08_2025/8du4_27715.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/08_2025/8du4_27715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8du4_27715/08_2025/8du4_27715.map"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

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

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.72, per 1000 atoms: 0.21
  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: 1.45
  Conformation dependent library (CDL) restraints added in 653.0 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 2.34
  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: 3.13

  Time building geometry restraints manager: 1.97 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=" CB  THR F  73 "
       pdb=" CG2 THR F  73 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.15e+00
  bond pdb=" CB  GLN F  27 "
       pdb=" CG  GLN F  27 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.95e+00
  bond pdb=" C3'  DC J 276 "
       pdb=" O3'  DC J 276 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.90e+00
  bond pdb=" CA  HIS F  75 "
       pdb=" CB  HIS F  75 "
    ideal  model  delta    sigma   weight residual
    1.525  1.543 -0.019 1.36e-02 5.41e+03 1.86e+00
  bond pdb=" C3'  DG J 244 "
       pdb=" O3'  DG J 244 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.80e+00
  ... (remaining 18330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.75: 25878
        2.75 -     5.51: 158
        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=" 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=" N   VAL N 249 "
        pdb=" CA  VAL N 249 "
        pdb=" C   VAL N 249 "
      ideal   model   delta    sigma   weight residual
     112.96  108.82    4.14 1.00e+00 1.00e+00 1.72e+01
  angle pdb=" CA  LEU N 185 "
        pdb=" CB  LEU N 185 "
        pdb=" CG  LEU N 185 "
      ideal   model   delta    sigma   weight residual
     116.30  130.07  -13.77 3.50e+00 8.16e-02 1.55e+01
  angle pdb=" CA  ASP N 149 "
        pdb=" C   ASP N 149 "
        pdb=" N   ASP N 150 "
      ideal   model   delta    sigma   weight residual
     119.98  116.71    3.27 8.50e-01 1.38e+00 1.48e+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: 2522
       0.053 -    0.106: 392
       0.106 -    0.159: 54
       0.159 -    0.211: 2
       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:                  0.010
  Normalize map: mean=0, sd=1:             2.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.020
  Process input model:                     17.110
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5076
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      :  0.004   0.048  18335  Z= 0.177
  Angle     :  0.690  13.768  26055  Z= 0.403
  Chirality :  0.040   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 aren 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
  covalent geometry    : bond        0.00370 (18335)
  covalent geometry    : angle       0.69000 (26055)
  hydrogen bonds       : bond        0.11928 (  859)
  hydrogen bonds       : angle       5.72708 ( 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  : 0.494 
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: 0.7301 (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: 0.1371
  time to fit residues: 22.6900
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  : 0.471 
-------------------------------------------------------------------------------
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:   10.0000
   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:    3.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    3.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
L 130 ASN
N 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.243482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.221462 restraints weight = 62727.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.224499 restraints weight = 89247.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.226064 restraints weight = 30306.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.227114 restraints weight = 17019.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.227204 restraints weight = 14014.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.4612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4612 r_free = 0.4612    target_work(ls_wunit_k1) = 0.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4612 r_free = 0.4612    target_work(ls_wunit_k1) = 0.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
r_final: 0.4612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5673
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.083  18335  Z= 0.392
  Angle     :  1.016  14.159  26055  Z= 0.553
  Chirality :  0.056   0.335   2972
  Planarity :  0.009   0.107   2279
  Dihedral  : 30.034 175.596   4809
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.21 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  6.62 %
    Allowed  : 15.90 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.21), residues: 1418
  helix: -0.85 (0.21), residues: 515
  sheet: -1.19 (0.38), residues: 191
  loop : -2.48 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG G  88 
 TYR   0.046   0.004   TYR B  98 
 PHE   0.025   0.003   PHE A  84 
 TRP   0.014   0.002   TRP L 330 
 HIS   0.014   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00919 (18335)
  covalent geometry    : angle       1.01594 (26055)
  hydrogen bonds       : bond        0.10030 (  859)
  hydrogen bonds       : angle       5.52577 ( 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
  167 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 86
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8837 (tt0)
REVERT: A  131 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7894 (ttp80)
REVERT: D   76 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7826 (mtp180)
REVERT: D   92 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8644 (tt0)
REVERT: H   34 TYR cc_start: 0.1119 (OUTLIER) cc_final: 0.0658 (m-10)
REVERT: H   58 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6023 (tt)
REVERT: L  130 ASN cc_start: 0.3074 (OUTLIER) cc_final: 0.2048 (t0)
REVERT: N   65 HIS cc_start: 0.3786 (OUTLIER) cc_final: 0.3511 (m90)
REVERT: N  167 TYR cc_start: 0.2504 (OUTLIER) cc_final: 0.1428 (m-10)
REVERT: N  259 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5746 (t80)
  outliers start: 81
  outliers final: 37
  residues processed: 162
  average time/residue: 0.1254
  time to fit residues: 30.0825
Evaluate side-chains
  118 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 72
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   66 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 C residue   16 THR
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   92 GLN
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   34 ILE
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   64 GLU
Chi-restraints excluded: chain H residue   34 TYR
Chi-restraints excluded: chain H residue   36 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 H residue   95 VAL
Chi-restraints excluded: chain L residue  130 ASN
Chi-restraints excluded: chain L residue  155 ILE
Chi-restraints excluded: chain L residue  237 THR
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   74 TRP
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  168 THR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  313 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 163 optimal weight:    7.9990
   chunk 145 optimal weight:   20.0000
   chunk 53 optimal weight:    0.5980
   chunk 112 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 134 optimal weight:   20.0000
   chunk 3 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 143 optimal weight:    0.6980
   chunk 160 optimal weight:   20.0000
   overall best weight:    1.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
E  93 GLN
E 113 HIS
F  25 ASN
** L 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4862 r_free = 0.4862 target = 0.243907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.210602 restraints weight = 67325.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.209011 restraints weight = 80680.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.208083 restraints weight = 57271.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.207563 restraints weight = 57685.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.206763 restraints weight = 47141.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4448 r_free = 0.4448    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4448 r_free = 0.4448    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.4448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6092
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  18335  Z= 0.233
  Angle     :  0.710  13.513  26055  Z= 0.397
  Chirality :  0.044   0.188   2972
  Planarity :  0.006   0.107   2279
  Dihedral  : 29.681 175.150   4801
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.45 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.21), residues: 1418
  helix: -0.13 (0.22), residues: 519
  sheet: -1.21 (0.36), residues: 214
  loop : -2.42 (0.22), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  77 
 TYR   0.024   0.002   TYR B  98 
 PHE   0.026   0.002   PHE A  84 
 TRP   0.015   0.001   TRP L 286 
 HIS   0.012   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (18335)
  covalent geometry    : angle       0.70971 (26055)
  hydrogen bonds       : bond        0.06585 (  859)
  hydrogen bonds       : angle       4.61235 ( 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
  147 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 90
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8390 (tt0)
REVERT: D   98 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: G   65 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7091 (mp)
REVERT: H   58 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7705 (tt)
REVERT: H  110 GLU cc_start: 0.5597 (OUTLIER) cc_final: 0.5254 (tp30)
REVERT: L  182 ASP cc_start: 0.2391 (m-30) cc_final: 0.1454 (t70)
REVERT: N  166 ILE cc_start: -0.0793 (OUTLIER) cc_final: -0.1660 (mm)
REVERT: N  167 TYR cc_start: 0.2757 (OUTLIER) cc_final: 0.1412 (m-10)
REVERT: N  259 PHE cc_start: 0.6222 (OUTLIER) cc_final: 0.5685 (t80)
  outliers start: 57
  outliers final: 24
  residues processed: 140
  average time/residue: 0.1292
  time to fit residues: 26.1776
Evaluate side-chains
  110 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
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 C residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain H residue   49 THR
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain L residue  237 THR
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  166 ILE
Chi-restraints excluded: chain N residue  167 TYR
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  266 ILE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 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:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 115 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 160 optimal weight:    0.0980
   chunk 138 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 170 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.242533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.213759 restraints weight = 78507.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.212675 restraints weight = 77693.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.210785 restraints weight = 56841.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.210278 restraints weight = 58145.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.210000 restraints weight = 47380.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4506 r_free = 0.4506    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4506 r_free = 0.4506    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.4506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5973
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18335  Z= 0.182
  Angle     :  0.629  11.248  26055  Z= 0.359
  Chirality :  0.041   0.262   2972
  Planarity :  0.005   0.059   2279
  Dihedral  : 29.303 175.269   4797
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 20.02 %
    Favored  : 75.87 %
  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 aren not related in a simple way.
  whole: -1.61 (0.22), residues: 1418
  helix:  0.45 (0.22), residues: 517
  sheet: -1.00 (0.37), residues: 218
  loop : -2.36 (0.22), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  71 
 TYR   0.014   0.002   TYR F  98 
 PHE   0.017   0.002   PHE A  84 
 TRP   0.013   0.001   TRP L 286 
 HIS   0.013   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (18335)
  covalent geometry    : angle       0.62934 (26055)
  hydrogen bonds       : bond        0.05821 (  859)
  hydrogen bonds       : angle       4.25299 ( 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
  143 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 93
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8355 (tt0)
REVERT: C   72 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6361 (t0)
REVERT: C   74 LYS cc_start: 0.7893 (mppt) cc_final: 0.7392 (mmtp)
REVERT: D   98 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8486 (mp)
REVERT: E   83 ARG cc_start: 0.0379 (mmm160) cc_final: -0.0214 (mtp85)
REVERT: G   65 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7562 (mp)
REVERT: H  110 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5711 (mm-30)
REVERT: N   65 HIS cc_start: 0.3616 (OUTLIER) cc_final: 0.3070 (m90)
REVERT: N  166 ILE cc_start: -0.0934 (OUTLIER) cc_final: -0.1407 (mm)
REVERT: N  222 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6440 (mp)
REVERT: N  259 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5510 (t80)
  outliers start: 50
  outliers final: 26
  residues processed: 129
  average time/residue: 0.1474
  time to fit residues: 27.0797
Evaluate side-chains
  116 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 81
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   35 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  101 THR
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 F residue   43 VAL
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  293 ILE
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  166 ILE
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  248 LEU
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 152 optimal weight:    0.0980
   chunk 60 optimal weight:    0.7980
   chunk 130 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 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 = 0.4874 r_free = 0.4874 target = 0.244123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.215373 restraints weight = 79058.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.213890 restraints weight = 77726.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.212169 restraints weight = 53423.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.212312 restraints weight = 54829.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.212113 restraints weight = 43514.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
r_final: 0.4533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5921
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  18335  Z= 0.149
  Angle     :  0.571   8.760  26055  Z= 0.329
  Chirality :  0.039   0.178   2972
  Planarity :  0.004   0.055   2279
  Dihedral  : 29.106 174.817   4793
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.90 %
    Favored  : 75.14 %
  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 aren not related in a simple way.
  whole: -1.23 (0.22), residues: 1418
  helix:  0.89 (0.23), residues: 519
  sheet: -0.87 (0.37), residues: 218
  loop : -2.23 (0.22), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  83 
 TYR   0.012   0.001   TYR F  98 
 PHE   0.025   0.001   PHE E  84 
 TRP   0.014   0.001   TRP L 286 
 HIS   0.007   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (18335)
  covalent geometry    : angle       0.57091 (26055)
  hydrogen bonds       : bond        0.04891 (  859)
  hydrogen bonds       : angle       3.95012 ( 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
  135 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 87
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8275 (tt0)
REVERT: C   56 GLU cc_start: 0.8377 (tp30) cc_final: 0.7754 (mp0)
REVERT: C   74 LYS cc_start: 0.7992 (mppt) cc_final: 0.7686 (mmtp)
REVERT: G   65 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7730 (mp)
REVERT: H  110 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6102 (mm-30)
REVERT: N   65 HIS cc_start: 0.3562 (OUTLIER) cc_final: 0.3001 (m90)
REVERT: N  259 PHE cc_start: 0.6067 (OUTLIER) cc_final: 0.5467 (t80)
  outliers start: 48
  outliers final: 22
  residues processed: 127
  average time/residue: 0.1288
  time to fit residues: 24.1307
Evaluate side-chains
  102 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   78 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 158 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 118 optimal weight:    5.9990
   chunk 130 optimal weight:    9.9990
   chunk 49 optimal weight:    0.6980
   chunk 157 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 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 = 0.4855 r_free = 0.4855 target = 0.241702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.209464 restraints weight = 78450.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.208374 restraints weight = 81214.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.206308 restraints weight = 57566.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.206685 restraints weight = 50270.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.206319 restraints weight = 39464.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.4472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4472 r_free = 0.4472    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4472 r_free = 0.4472    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
r_final: 0.4472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6057
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18335  Z= 0.154
  Angle     :  0.568   7.560  26055  Z= 0.327
  Chirality :  0.039   0.150   2972
  Planarity :  0.004   0.051   2279
  Dihedral  : 28.964 175.318   4789
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.63 %
    Favored  : 74.90 %
  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 aren not related in a simple way.
  whole: -1.00 (0.22), residues: 1418
  helix:  1.08 (0.23), residues: 521
  sheet: -0.71 (0.36), residues: 231
  loop : -2.14 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  71 
 TYR   0.010   0.001   TYR F  98 
 PHE   0.026   0.002   PHE E  84 
 TRP   0.015   0.001   TRP L 286 
 HIS   0.010   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (18335)
  covalent geometry    : angle       0.56774 (26055)
  hydrogen bonds       : bond        0.05078 (  859)
  hydrogen bonds       : angle       3.85328 ( 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
  125 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 83
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   93 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8405 (tt0)
REVERT: C   16 THR cc_start: 0.6622 (OUTLIER) cc_final: 0.6397 (t)
REVERT: C   56 GLU cc_start: 0.8376 (tp30) cc_final: 0.7718 (mp0)
REVERT: C   72 ASP cc_start: 0.7450 (t0) cc_final: 0.7023 (t0)
REVERT: C   74 LYS cc_start: 0.8367 (mppt) cc_final: 0.7787 (mttm)
REVERT: E   97 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7962 (mp0)
REVERT: G   65 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7944 (mp)
REVERT: H  110 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6265 (mm-30)
REVERT: N   65 HIS cc_start: 0.3599 (OUTLIER) cc_final: 0.2985 (m90)
REVERT: N  259 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5433 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 117
  average time/residue: 0.1283
  time to fit residues: 22.1178
Evaluate side-chains
  109 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
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 C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   56 MET
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   66 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  144 VAL
Chi-restraints excluded: chain N residue  219 ASP
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 136 optimal weight:   20.0000
   chunk 149 optimal weight:   10.0000
   chunk 141 optimal weight:   20.0000
   chunk 156 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 0 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 148 optimal weight:    6.9990
   overall best weight:    3.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  38 ASN
** H  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 170 HIS
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.231025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.196217 restraints weight = 61011.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.194056 restraints weight = 71065.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.192061 restraints weight = 54500.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.191606 restraints weight = 49418.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.190544 restraints weight = 46736.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4292
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4292 r_free = 0.4292    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4292 r_free = 0.4292    target_work(ls_wunit_k1) = 0.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.4292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6446
moved from start:          0.6872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.099  18335  Z= 0.366
  Angle     :  0.884  12.423  26055  Z= 0.489
  Chirality :  0.053   0.396   2972
  Planarity :  0.007   0.066   2279
  Dihedral  : 29.776 174.444   4787
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.71 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 21.07 %
    Favored  : 74.66 %
  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 aren not related in a simple way.
  whole: -1.87 (0.21), residues: 1418
  helix: -0.09 (0.22), residues: 509
  sheet: -0.73 (0.37), residues: 218
  loop : -2.35 (0.22), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG O  72 
 TYR   0.035   0.003   TYR F  88 
 PHE   0.037   0.003   PHE E  84 
 TRP   0.012   0.002   TRP L 114 
 HIS   0.012   0.002   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00860 (18335)
  covalent geometry    : angle       0.88358 (26055)
  hydrogen bonds       : bond        0.09541 (  859)
  hydrogen bonds       : angle       5.07563 ( 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
  140 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 88
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8666 (tt0)
REVERT: A  131 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8348 (ttp80)
REVERT: E   97 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7762 (mp0)
REVERT: G  110 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8593 (t0)
REVERT: H   59 MET cc_start: 0.8462 (tpp) cc_final: 0.8176 (mmt)
REVERT: N  259 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.5441 (t80)
  outliers start: 52
  outliers final: 31
  residues processed: 133
  average time/residue: 0.1247
  time to fit residues: 24.2251
Evaluate side-chains
  108 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 72
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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   30 THR
Chi-restraints excluded: chain B residue   35 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   88 TYR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   62 LEU
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 G residue  110 ASN
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain N residue   49 VAL
Chi-restraints excluded: chain N residue   66 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  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Chi-restraints excluded: chain O residue   36 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 98 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 110 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 153 optimal weight:    9.9990
   chunk 147 optimal weight:    7.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
H  81 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4810 r_free = 0.4810 target = 0.236521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.204447 restraints weight = 72864.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.202942 restraints weight = 75352.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.200780 restraints weight = 55405.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.200746 restraints weight = 50492.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.200144 restraints weight = 42507.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.4423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.4423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6226
moved from start:          0.6881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  18335  Z= 0.168
  Angle     :  0.617   8.911  26055  Z= 0.353
  Chirality :  0.041   0.205   2972
  Planarity :  0.004   0.054   2279
  Dihedral  : 29.313 173.489   4787
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.76 %
    Favored  : 74.25 %
  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 aren not related in a simple way.
  whole: -1.27 (0.22), residues: 1418
  helix:  0.59 (0.22), residues: 528
  sheet: -0.65 (0.36), residues: 230
  loop : -2.16 (0.23), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.013   0.001   TYR F  98 
 PHE   0.016   0.001   PHE N 213 
 TRP   0.016   0.001   TRP L 286 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (18335)
  covalent geometry    : angle       0.61714 (26055)
  hydrogen bonds       : bond        0.05732 (  859)
  hydrogen bonds       : angle       4.13413 ( 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
  119 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8307 (tt0)
REVERT: C   56 GLU cc_start: 0.8270 (tp30) cc_final: 0.7713 (mp0)
REVERT: E   97 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: N  259 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5432 (t80)
  outliers start: 36
  outliers final: 21
  residues processed: 114
  average time/residue: 0.1179
  time to fit residues: 19.5673
Evaluate side-chains
  104 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain L residue  293 ILE
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  219 ASP
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 143 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 151 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 132 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 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 = 0.4815 r_free = 0.4815 target = 0.237055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.201505 restraints weight = 76841.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.199982 restraints weight = 77478.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.197525 restraints weight = 48680.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.196934 restraints weight = 52681.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.196197 restraints weight = 45038.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4375
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4375 r_free = 0.4375    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4375 r_free = 0.4375    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.4375
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6301
moved from start:          0.7066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18335  Z= 0.152
  Angle     :  0.578   7.456  26055  Z= 0.334
  Chirality :  0.039   0.148   2972
  Planarity :  0.004   0.050   2279
  Dihedral  : 29.002 175.256   4787
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 22.92 %
    Favored  : 74.50 %
  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 aren not related in a simple way.
  whole: -0.91 (0.23), residues: 1418
  helix:  1.08 (0.23), residues: 521
  sheet: -0.63 (0.36), residues: 236
  loop : -2.04 (0.23), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.011   0.001   TYR E  54 
 PHE   0.013   0.001   PHE N 213 
 TRP   0.013   0.001   TRP N  93 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (18335)
  covalent geometry    : angle       0.57802 (26055)
  hydrogen bonds       : bond        0.05092 (  859)
  hydrogen bonds       : angle       3.91793 ( 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
  122 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8298 (tt0)
REVERT: C   56 GLU cc_start: 0.8350 (tp30) cc_final: 0.7753 (mp0)
REVERT: E   97 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7943 (mp0)
REVERT: H   59 MET cc_start: 0.8407 (tpp) cc_final: 0.7951 (mmt)
REVERT: H  113 LYS cc_start: 0.7046 (mttm) cc_final: 0.6763 (mtmm)
REVERT: L  130 ASN cc_start: 0.3605 (p0) cc_final: 0.1318 (m-40)
REVERT: N  259 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5374 (t80)
  outliers start: 31
  outliers final: 24
  residues processed: 118
  average time/residue: 0.1419
  time to fit residues: 24.0285
Evaluate side-chains
  112 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain L residue  293 ILE
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  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  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:   20.0000
   chunk 144 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 87 optimal weight:    6.9990
   chunk 3 optimal weight:    0.4980
   chunk 116 optimal weight:   20.0000
   chunk 47 optimal weight:    0.9980
   chunk 114 optimal weight:    9.9990
   chunk 132 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 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 = 0.4804 r_free = 0.4804 target = 0.235845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.203813 restraints weight = 76227.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.201941 restraints weight = 79866.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.199360 restraints weight = 59754.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.199342 restraints weight = 57159.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.198251 restraints weight = 50871.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.4396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4395 r_free = 0.4395    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4395 r_free = 0.4395    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.4395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6249
moved from start:          0.7313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  18335  Z= 0.165
  Angle     :  0.593   7.796  26055  Z= 0.339
  Chirality :  0.040   0.159   2972
  Planarity :  0.004   0.054   2279
  Dihedral  : 28.999 177.761   4785
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 23.08 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.23), residues: 1418
  helix:  1.12 (0.23), residues: 520
  sheet: -0.62 (0.36), residues: 232
  loop : -1.98 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  71 
 TYR   0.013   0.001   TYR E  54 
 PHE   0.013   0.001   PHE H  62 
 TRP   0.012   0.001   TRP L 286 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (18335)
  covalent geometry    : angle       0.59268 (26055)
  hydrogen bonds       : bond        0.05293 (  859)
  hydrogen bonds       : angle       3.91022 ( 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
  115 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8229 (tt0)
REVERT: C   56 GLU cc_start: 0.8377 (tp30) cc_final: 0.7776 (mp0)
REVERT: H   59 MET cc_start: 0.8559 (tpp) cc_final: 0.7942 (mmt)
REVERT: H  113 LYS cc_start: 0.7430 (mttm) cc_final: 0.7173 (mtmm)
REVERT: L  130 ASN cc_start: 0.3689 (p0) cc_final: 0.1419 (m-40)
REVERT: N  259 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5411 (t80)
  outliers start: 28
  outliers final: 22
  residues processed: 112
  average time/residue: 0.1426
  time to fit residues: 22.8851
Evaluate side-chains
  108 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  110 GLU
Chi-restraints excluded: chain H residue  117 CYS
Chi-restraints excluded: chain L residue  293 ILE
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  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  317 VAL
Chi-restraints excluded: chain O residue    9 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 148 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 69 optimal weight:    0.4980
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.6584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 116 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 = 0.4770 r_free = 0.4770 target = 0.232316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.199043 restraints weight = 64211.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.196071 restraints weight = 72994.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.194807 restraints weight = 60812.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.195053 restraints weight = 54343.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.194643 restraints weight = 43431.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4357 r_free = 0.4357    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4356 r_free = 0.4356    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.4356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
moved from start:          0.7863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  18335  Z= 0.217
  Angle     :  0.673   9.015  26055  Z= 0.380
  Chirality :  0.043   0.225   2972
  Planarity :  0.005   0.048   2279
  Dihedral  : 29.217 178.320   4785
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.89 %
    Favored  : 74.01 %
  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 aren not related in a simple way.
  whole: -1.09 (0.22), residues: 1418
  helix:  0.82 (0.23), residues: 523
  sheet: -0.61 (0.35), residues: 243
  loop : -2.12 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E  72 
 TYR   0.020   0.002   TYR F  88 
 PHE   0.017   0.002   PHE H  62 
 TRP   0.011   0.001   TRP L 286 
 HIS   0.010   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (18335)
  covalent geometry    : angle       0.67256 (26055)
  hydrogen bonds       : bond        0.06421 (  859)
  hydrogen bonds       : angle       4.20580 ( 2148)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2241.69 seconds
wall clock time: 39 minutes 35.53 seconds (2375.53 seconds total)