Starting phenix.real_space_refine
on Thu Jun 19 13:48:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8du4_27715/06_2025/8du4_27715.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8du4_27715/06_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8du4_27715/06_2025/8du4_27715.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8du4_27715/06_2025/8du4_27715.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8du4_27715/06_2025/8du4_27715.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8du4_27715/06_2025/8du4_27715.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.55, per 1000 atoms: 0.66
  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: 4.17
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 6.98
  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: 6.35

  Time building geometry restraints manager: 5.06 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:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.150
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     45.500
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.660
-------------------------------------------------------------------------------
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 : 14.07
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.020   0.002   TRP N  74 
 HIS   0.025   0.001   HIS F  75 
 PHE   0.017   0.002   PHE E  67 
 TYR   0.017   0.002   TYR E  54 
 ARG   0.008   0.001   ARG F  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11928 (  859)
  hydrogen bonds       : angle       5.72708 ( 2148)
  covalent geometry    : bond        0.00370 (18335)
  covalent geometry    : angle       0.69000 (26055)

*********************** 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  : 1.932 
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: 0.3846
  time to fit residues: 63.7755
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  : 1.374 
-------------------------------------------------------------------------------
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 141 optimal weight:    0.5980
   chunk 126 optimal weight:   40.0000
   chunk 70 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 130 optimal weight:    9.9990
   chunk 50 optimal weight:    0.4980
   chunk 79 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 151 optimal weight:    0.0470
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
L 287 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 = 0.5002 r_free = 0.5002 target = 0.258848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.239888 restraints weight = 71602.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.242918 restraints weight = 90774.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.245453 restraints weight = 31992.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4824 r_free = 0.4824    target_work(ls_wunit_k1) = 0.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4823 r_free = 0.4823    target_work(ls_wunit_k1) = 0.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
r_final: 0.4823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5068
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18335  Z= 0.149
  Angle     :  0.602  10.629  26055  Z= 0.341
  Chirality :  0.039   0.165   2972
  Planarity :  0.004   0.052   2279
  Dihedral  : 28.984 167.257   4809
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.82 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.22), residues: 1418
  helix:  0.58 (0.23), residues: 515
  sheet: -1.03 (0.39), residues: 202
  loop : -2.15 (0.22), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 286 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.014   0.001   PHE E  67 
 TYR   0.018   0.001   TYR F  98 
 ARG   0.005   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05051 (  859)
  hydrogen bonds       : angle       4.17373 ( 2148)
  covalent geometry    : bond        0.00318 (18335)
  covalent geometry    : angle       0.60195 (26055)

*********************** 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
  123 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 86
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
REVERT: F   74 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5830 (mt-10)
REVERT: H   93 THR cc_start: 0.7103 (t) cc_final: 0.5133 (p)
REVERT: L  182 ASP cc_start: 0.2536 (m-30) cc_final: 0.1143 (t70)
  outliers start: 37
  outliers final: 19
  residues processed: 117
  average time/residue: 0.2764
  time to fit residues: 49.2824
Evaluate side-chains
  99 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   82 THR
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 E residue   60 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain L residue  155 ILE
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  186 VAL
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  287 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 145 optimal weight:   20.0000
   chunk 26 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 147 optimal weight:    0.4980
   chunk 135 optimal weight:    0.0670
   chunk 157 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.0320

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4959 r_free = 0.4959 target = 0.254136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.234086 restraints weight = 59883.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.236888 restraints weight = 91870.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.238456 restraints weight = 33103.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4763 r_free = 0.4763    target_work(ls_wunit_k1) = 0.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4763 r_free = 0.4763    target_work(ls_wunit_k1) = 0.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.4763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5268
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18335  Z= 0.174
  Angle     :  0.615   8.120  26055  Z= 0.349
  Chirality :  0.040   0.168   2972
  Planarity :  0.005   0.046   2279
  Dihedral  : 29.086 169.979   4797
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 16.22 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.22), residues: 1418
  helix:  0.69 (0.23), residues: 515
  sheet: -1.27 (0.34), residues: 244
  loop : -2.14 (0.23), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 286 
 HIS   0.009   0.001   HIS F  75 
 PHE   0.021   0.001   PHE E  67 
 TYR   0.018   0.002   TYR H  39 
 ARG   0.007   0.000   ARG G  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05380 (  859)
  hydrogen bonds       : angle       4.08367 ( 2148)
  covalent geometry    : bond        0.00382 (18335)
  covalent geometry    : angle       0.61502 (26055)

*********************** 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
  127 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 80
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8359 (tt0)
REVERT: E   67 PHE cc_start: 0.2824 (OUTLIER) cc_final: 0.2615 (t80)
REVERT: N   65 HIS cc_start: 0.3427 (OUTLIER) cc_final: 0.2790 (m90)
REVERT: O   69 LEU cc_start: 0.0653 (OUTLIER) cc_final: 0.0106 (mp)
  outliers start: 47
  outliers final: 29
  residues processed: 122
  average time/residue: 0.3137
  time to fit residues: 57.5535
Evaluate side-chains
  106 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 73
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   30 THR
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 C residue   33 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   67 PHE
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain N residue   65 HIS
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  286 LEU
Chi-restraints excluded: chain N residue  287 VAL
Chi-restraints excluded: chain N residue  290 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 103 optimal weight:   10.0000
   chunk 157 optimal weight:    4.9990
   chunk 64 optimal weight:    0.1980
   chunk 131 optimal weight:    6.9990
   chunk 112 optimal weight:    9.9990
   chunk 143 optimal weight:    0.5980
   chunk 133 optimal weight:    0.2980
   chunk 54 optimal weight:    0.0370
   chunk 106 optimal weight:    9.9990
   chunk 156 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6260

-------------------------------------------------------------------------------
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**
E 113 HIS
N 170 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4968 r_free = 0.4968 target = 0.255165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.235787 restraints weight = 64050.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4781 r_free = 0.4781 target = 0.238776 restraints weight = 91817.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.240665 restraints weight = 31481.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4783 r_free = 0.4783    target_work(ls_wunit_k1) = 0.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4783 r_free = 0.4783    target_work(ls_wunit_k1) = 0.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.4783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5226
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18335  Z= 0.141
  Angle     :  0.555   8.343  26055  Z= 0.319
  Chirality :  0.038   0.146   2972
  Planarity :  0.004   0.047   2279
  Dihedral  : 28.896 170.313   4795
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.92 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.23), residues: 1418
  helix:  0.99 (0.23), residues: 522
  sheet: -1.10 (0.35), residues: 239
  loop : -2.10 (0.23), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 286 
 HIS   0.011   0.001   HIS F  75 
 PHE   0.012   0.001   PHE N 213 
 TYR   0.015   0.001   TYR F  98 
 ARG   0.006   0.000   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04447 (  859)
  hydrogen bonds       : angle       3.76924 ( 2148)
  covalent geometry    : bond        0.00304 (18335)
  covalent geometry    : angle       0.55465 (26055)

*********************** 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
  123 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 87
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8142 (tt0)
REVERT: C   71 ARG cc_start: 0.6517 (tmm160) cc_final: 0.5835 (ttm170)
REVERT: E   65 LEU cc_start: 0.7146 (tp) cc_final: 0.6799 (tp)
REVERT: E   83 ARG cc_start: 0.0489 (mtp180) cc_final: -0.0115 (ttm170)
REVERT: H   46 HIS cc_start: 0.0906 (m90) cc_final: 0.0528 (m90)
REVERT: H   58 ILE cc_start: 0.5571 (OUTLIER) cc_final: 0.4995 (tt)
REVERT: H   59 MET cc_start: 0.1749 (ptp) cc_final: 0.0907 (tpt)
REVERT: L  182 ASP cc_start: 0.2604 (m-30) cc_final: 0.1396 (t70)
REVERT: N   61 ILE cc_start: 0.4242 (mt) cc_final: 0.4023 (tp)
REVERT: N   65 HIS cc_start: 0.3316 (OUTLIER) cc_final: 0.2671 (m90)
REVERT: N  134 MET cc_start: 0.2784 (ttt) cc_final: 0.2529 (mtp)
REVERT: O   69 LEU cc_start: 0.0239 (OUTLIER) cc_final: -0.0444 (mp)
  outliers start: 36
  outliers final: 18
  residues processed: 119
  average time/residue: 0.3532
  time to fit residues: 61.0436
Evaluate side-chains
  103 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   34 ILE
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   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain N residue   65 HIS
Chi-restraints excluded: chain N residue   92 GLN
Chi-restraints excluded: chain N residue  222 ILE
Chi-restraints excluded: chain N residue  286 LEU
Chi-restraints excluded: chain N residue  290 LEU
Chi-restraints excluded: chain O residue   69 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0870
   chunk 96 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 141 optimal weight:   20.0000
   chunk 123 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9980
   overall best weight:    2.8164

-------------------------------------------------------------------------------
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**
C  73 ASN
L 130 ASN
L 170 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.242400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.211912 restraints weight = 73382.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.210716 restraints weight = 79768.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.208472 restraints weight = 53513.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4464 r_free = 0.4464    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4463 r_free = 0.4463    target_work(ls_wunit_k1) = 0.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.4463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6033
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.097  18335  Z= 0.354
  Angle     :  0.892  13.131  26055  Z= 0.487
  Chirality :  0.050   0.269   2972
  Planarity :  0.008   0.107   2279
  Dihedral  : 29.635 176.546   4793
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.57 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 18.97 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.94 (0.22), residues: 1418
  helix: -0.24 (0.22), residues: 507
  sheet: -1.06 (0.35), residues: 237
  loop : -2.21 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP L 114 
 HIS   0.023   0.002   HIS F  75 
 PHE   0.028   0.002   PHE H  67 
 TYR   0.047   0.004   TYR B  98 
 ARG   0.008   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08851 (  859)
  hydrogen bonds       : angle       4.91116 ( 2148)
  covalent geometry    : bond        0.00820 (18335)
  covalent geometry    : angle       0.89192 (26055)

*********************** 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
  149 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 90
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8705 (tt0)
REVERT: A  131 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8370 (ttp80)
REVERT: D   98 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8529 (mp)
REVERT: E   65 LEU cc_start: 0.7920 (tp) cc_final: 0.7324 (mt)
REVERT: E   83 ARG cc_start: 0.1213 (OUTLIER) cc_final: 0.0854 (mtp85)
REVERT: E   97 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7528 (mp0)
REVERT: G   75 LYS cc_start: 0.4377 (mmtm) cc_final: 0.4053 (tppt)
REVERT: G   78 ILE cc_start: 0.1255 (OUTLIER) cc_final: 0.0935 (mt)
REVERT: H   58 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6459 (pt)
REVERT: L  130 ASN cc_start: 0.3269 (OUTLIER) cc_final: 0.2195 (t0)
REVERT: N   65 HIS cc_start: 0.3645 (OUTLIER) cc_final: 0.3243 (m90)
REVERT: N  259 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5776 (t80)
REVERT: O   69 LEU cc_start: 0.0271 (OUTLIER) cc_final: -0.0252 (mp)
  outliers start: 59
  outliers final: 25
  residues processed: 143
  average time/residue: 0.3296
  time to fit residues: 68.6471
Evaluate side-chains
  107 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 71
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
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   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   83 ARG
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   57 TYR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 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 L residue  130 ASN
Chi-restraints excluded: chain L residue  267 SER
Chi-restraints excluded: chain N residue   65 HIS
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  286 LEU
Chi-restraints excluded: chain N residue  287 VAL
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain O residue   69 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 165 optimal weight:    0.9990
   chunk 164 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 158 optimal weight:    0.0570
   chunk 161 optimal weight:    4.9990
   chunk 156 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 64 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7902

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
N  67 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 = 0.4882 r_free = 0.4882 target = 0.245614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.218138 restraints weight = 80626.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.216276 restraints weight = 77016.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.214079 restraints weight = 59613.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.4555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4556 r_free = 0.4556    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4556 r_free = 0.4556    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.4556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.4438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  18335  Z= 0.156
  Angle     :  0.596   8.827  26055  Z= 0.343
  Chirality :  0.040   0.150   2972
  Planarity :  0.004   0.079   2279
  Dihedral  : 29.217 174.018   4789
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.66 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.22), residues: 1418
  helix:  0.52 (0.22), residues: 515
  sheet: -0.89 (0.36), residues: 238
  loop : -2.19 (0.23), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 286 
 HIS   0.008   0.001   HIS F  75 
 PHE   0.015   0.001   PHE N 213 
 TYR   0.015   0.001   TYR F  98 
 ARG   0.015   0.000   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05265 (  859)
  hydrogen bonds       : angle       4.01543 ( 2148)
  covalent geometry    : bond        0.00339 (18335)
  covalent geometry    : angle       0.59635 (26055)

*********************** 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
  126 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 87
  time to evaluate  : 1.530 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8086 (tt0)
REVERT: C   72 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6994 (t0)
REVERT: D   98 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8433 (mp)
REVERT: E   65 LEU cc_start: 0.7909 (tp) cc_final: 0.7644 (mt)
REVERT: H   56 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.3007 (ptp)
REVERT: H   58 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6795 (tt)
REVERT: N   65 HIS cc_start: 0.3652 (OUTLIER) cc_final: 0.3380 (m90)
REVERT: N  259 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5618 (t80)
  outliers start: 39
  outliers final: 15
  residues processed: 120
  average time/residue: 0.3521
  time to fit residues: 62.3807
Evaluate side-chains
  98 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   98 LEU
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 H residue   56 MET
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain N residue   65 HIS
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  287 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 155 optimal weight:    0.2980
   chunk 136 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 128 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 154 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
C  38 ASN
C  73 ASN
H 106 HIS
L 130 ASN
** 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 = 0.4804 r_free = 0.4804 target = 0.237419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.212632 restraints weight = 51442.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.214931 restraints weight = 92152.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.216756 restraints weight = 34464.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4536 r_free = 0.4536    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4536 r_free = 0.4536    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.4536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5905
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  18335  Z= 0.246
  Angle     :  0.730   9.171  26055  Z= 0.408
  Chirality :  0.045   0.241   2972
  Planarity :  0.006   0.062   2279
  Dihedral  : 29.260 175.923   4789
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 20.18 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.22), residues: 1418
  helix:  0.35 (0.22), residues: 517
  sheet: -0.88 (0.36), residues: 235
  loop : -2.16 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 286 
 HIS   0.015   0.002   HIS H 106 
 PHE   0.025   0.002   PHE H  62 
 TYR   0.022   0.002   TYR F  88 
 ARG   0.014   0.001   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07566 (  859)
  hydrogen bonds       : angle       4.44980 ( 2148)
  covalent geometry    : bond        0.00564 (18335)
  covalent geometry    : angle       0.72996 (26055)

*********************** 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
  133 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 83
  time to evaluate  : 1.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8670 (tt0)
REVERT: A  131 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8283 (ttp80)
REVERT: B   35 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (mmt90)
REVERT: D   80 TYR cc_start: 0.7562 (t80) cc_final: 0.7347 (t80)
REVERT: D   98 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8531 (mp)
REVERT: E   65 LEU cc_start: 0.7917 (tp) cc_final: 0.7318 (mt)
REVERT: E   97 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7677 (mp0)
REVERT: G   62 ILE cc_start: 0.7749 (mm) cc_final: 0.7495 (tt)
REVERT: N   65 HIS cc_start: 0.3644 (OUTLIER) cc_final: 0.3283 (m90)
REVERT: N  259 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5498 (t80)
  outliers start: 50
  outliers final: 33
  residues processed: 125
  average time/residue: 0.3292
  time to fit residues: 62.0202
Evaluate side-chains
  113 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 73
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
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   35 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   38 ASN
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   31 LYS
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   78 ARG
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 H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue  106 HIS
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  130 ASN
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  318 VAL
Chi-restraints excluded: chain O residue    5 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 72 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0370
   chunk 154 optimal weight:    5.9990
   chunk 132 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 143 optimal weight:    8.9990
   chunk 48 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.4858 r_free = 0.4858 target = 0.242318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.218271 restraints weight = 60477.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.221271 restraints weight = 88425.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.223681 restraints weight = 30678.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.4614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4615 r_free = 0.4615    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4615 r_free = 0.4615    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.4615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5747
moved from start:          0.5730

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= 0.143
  Angle     :  0.581   9.924  26055  Z= 0.333
  Chirality :  0.039   0.147   2972
  Planarity :  0.004   0.051   2279
  Dihedral  : 29.006 174.593   4789
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.23 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.22), residues: 1418
  helix:  0.96 (0.23), residues: 519
  sheet: -0.69 (0.36), residues: 244
  loop : -2.02 (0.23), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 286 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.015   0.001   PHE N 213 
 TYR   0.012   0.001   TYR H 118 
 ARG   0.004   0.000   ARG H  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05027 (  859)
  hydrogen bonds       : angle       3.89441 ( 2148)
  covalent geometry    : bond        0.00306 (18335)
  covalent geometry    : angle       0.58123 (26055)

*********************** 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
  114 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 78
  time to evaluate  : 2.031 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.9087 (tt) cc_final: 0.8830 (tt)
REVERT: A   93 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8139 (tt0)
REVERT: B   35 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7537 (mmt90)
REVERT: C   16 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6253 (t)
REVERT: N   65 HIS cc_start: 0.3562 (OUTLIER) cc_final: 0.2940 (m90)
REVERT: N  259 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5468 (t80)
  outliers start: 36
  outliers final: 18
  residues processed: 108
  average time/residue: 0.3880
  time to fit residues: 62.9268
Evaluate side-chains
  97 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 2.050 
-------------------------------------------------------------------------------
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   35 ARG
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain F residue   35 ARG
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  100 VAL
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  293 ILE
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  318 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 151 optimal weight:    0.0270
   chunk 144 optimal weight:    0.5980
   chunk 102 optimal weight:    8.9990
   chunk 139 optimal weight:    1.9990
   chunk 122 optimal weight:   30.0000
   chunk 84 optimal weight:   10.0000
   chunk 68 optimal weight:    0.3980
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.2042

-------------------------------------------------------------------------------
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
F  25 ASN
** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 274 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.238410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.205434 restraints weight = 73092.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.201746 restraints weight = 67106.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.198046 restraints weight = 52911.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4397 r_free = 0.4397    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4397 r_free = 0.4397    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.4397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
moved from start:          0.6153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  18335  Z= 0.182
  Angle     :  0.618  11.230  26055  Z= 0.352
  Chirality :  0.040   0.161   2972
  Planarity :  0.005   0.048   2279
  Dihedral  : 28.946 175.656   4787
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.22), residues: 1418
  helix:  0.87 (0.22), residues: 519
  sheet: -0.65 (0.35), residues: 250
  loop : -1.98 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L 286 
 HIS   0.009   0.001   HIS F  75 
 PHE   0.041   0.002   PHE E  84 
 TYR   0.016   0.002   TYR F  88 
 ARG   0.005   0.001   ARG E  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05752 (  859)
  hydrogen bonds       : angle       3.98035 ( 2148)
  covalent geometry    : bond        0.00411 (18335)
  covalent geometry    : angle       0.61813 (26055)

*********************** 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
  113 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 2.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8296 (tt0)
REVERT: E   97 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7863 (mp0)
REVERT: L  107 ASP cc_start: 0.3490 (m-30) cc_final: 0.2111 (t0)
REVERT: N   65 HIS cc_start: 0.3580 (OUTLIER) cc_final: 0.3033 (m90)
REVERT: N  259 PHE cc_start: 0.6051 (OUTLIER) cc_final: 0.5406 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 109
  average time/residue: 0.5064
  time to fit residues: 86.6404
Evaluate side-chains
  99 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 1.907 
-------------------------------------------------------------------------------
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  107 VAL
Chi-restraints excluded: chain D residue   58 ILE
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   35 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue  293 ILE
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  301 VAL
Chi-restraints excluded: chain N residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 163 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0050
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0970
   chunk 102 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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**
G  38 ASN
H  60 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 = 0.4862 r_free = 0.4862 target = 0.242138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.218452 restraints weight = 55176.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.221589 restraints weight = 90216.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.222912 restraints weight = 32339.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4616 r_free = 0.4616    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4616 r_free = 0.4616    target_work(ls_wunit_k1) = 0.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.4616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5738
moved from start:          0.6318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  18335  Z= 0.135
  Angle     :  0.558   8.409  26055  Z= 0.322
  Chirality :  0.038   0.170   2972
  Planarity :  0.004   0.048   2279
  Dihedral  : 28.720 176.083   4787
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 22.60 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.23), residues: 1418
  helix:  1.28 (0.23), residues: 520
  sheet: -0.58 (0.36), residues: 242
  loop : -1.90 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 286 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.031   0.001   PHE E  84 
 TYR   0.011   0.001   TYR F  98 
 ARG   0.008   0.000   ARG O  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  859)
  hydrogen bonds       : angle       3.67196 ( 2148)
  covalent geometry    : bond        0.00286 (18335)
  covalent geometry    : angle       0.55812 (26055)

********************** 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
  109 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7376 (tmm160)
REVERT: E   97 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7941 (mp0)
REVERT: L  107 ASP cc_start: 0.3544 (m-30) cc_final: 0.2244 (t0)
REVERT: N   65 HIS cc_start: 0.3345 (OUTLIER) cc_final: 0.2844 (m90)
REVERT: N  259 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5489 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 109
  average time/residue: 0.5164
  time to fit residues: 85.6858
Evaluate side-chains
  102 residues out of total 1227 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 2.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain E residue   97 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue   58 ILE
Chi-restraints excluded: chain H residue   86 ILE
Chi-restraints excluded: chain L residue  293 ILE
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  222 ILE
Chi-restraints excluded: chain N residue  259 PHE
Chi-restraints excluded: chain N residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 167
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 155 optimal weight:    0.2980
   chunk 134 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 116 optimal weight:    0.0770
   chunk 100 optimal weight:   30.0000
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.5538

-------------------------------------------------------------------------------
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**
H  81 ASN
H  92 GLN
** 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 = 0.4850 r_free = 0.4850 target = 0.240860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.216820 restraints weight = 59378.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.219831 restraints weight = 93986.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.221823 restraints weight = 31971.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4597 r_free = 0.4597    target_work(ls_wunit_k1) = 0.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4597 r_free = 0.4597    target_work(ls_wunit_k1) = 0.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.4597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5783
moved from start:          0.6462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18335  Z= 0.140
  Angle     :  0.563   9.197  26055  Z= 0.322
  Chirality :  0.038   0.153   2972
  Planarity :  0.004   0.045   2279
  Dihedral  : 28.674 177.754   4787
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 22.52 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.23), residues: 1418
  helix:  1.34 (0.23), residues: 521
  sheet: -0.50 (0.36), residues: 247
  loop : -1.90 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L 286 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.037   0.001   PHE E  84 
 TYR   0.011   0.001   TYR E  54 
 ARG   0.007   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  859)
  hydrogen bonds       : angle       3.64530 ( 2148)
  covalent geometry    : bond        0.00303 (18335)
  covalent geometry    : angle       0.56301 (26055)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5610.07 seconds
wall clock time: 101 minutes 34.27 seconds (6094.27 seconds total)