Starting phenix.real_space_refine
on Fri Mar  6 00:05:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mbm_23738/03_2026/7mbm_23738.cif"
  }
  resolution = 4.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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 8542 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S      57      5.16       5
     C   11568      2.51       5
     N    3596      2.21       5
     O    4246      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19757
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2665
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 14, 'TRANS': 324}
    Chain: "B"
      Number of atoms: 2326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2326
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 8, 'TRANS': 291}
    Chain: "C"
      Number of atoms: 1435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 1435
          Classifications: {'peptide': 179}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 173}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 1399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1399
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 12, 'TRANS': 163}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "H"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "I"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 825
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "J"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 741
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "K"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "L"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "M"
      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: "N"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "O"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "P"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 4.26, per 1000 atoms: 0.22
  Number of scatterers: 19757
  At special positions: 0
  Unit cell: (142.04, 121.9, 156.88, 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      57     16.00
     P     290     15.00
     O    4246      8.00
     N    3596      7.00
     C   11568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.30
  Conformation dependent library (CDL) restraints added in 596.8 milliseconds
  

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3260

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 27 sheets defined
      32.7% alpha, 11.8% beta
      138 base pairs and 238 stacking pairs defined.
    Time for finding SS restraints: 3.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 228 through 234
    Processing helix  chain 'C' and resid 3815 through 3828
      removed outlier: 3.725A  pdb=" N   ARG C3819 " --> pdb=" O   PRO C3815 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   HIS C3822 " --> pdb=" O   MET C3818 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   LYS C3824 " --> pdb=" O   PHE C3820 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   LYS C3825 " --> pdb=" O   ARG C3821 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS C3828 " --> pdb=" O   LYS C3824 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3866 through 3879
      removed outlier: 3.636A  pdb=" N   LYS C3870 " --> pdb=" O   ILE C3866 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3900 through 3904
      removed outlier: 4.180A  pdb=" N   ARG C3903 " --> pdb=" O   ASN C3900 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   PHE C3904 " --> pdb=" O   ALA C3901 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 3900 through 3904'
    Processing helix  chain 'D' and resid 368 through 372
      removed outlier: 3.776A  pdb=" N   GLY D 371 " --> pdb=" O   SER D 368 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   THR D 372 " --> pdb=" O   LYS D 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 368 through 372'
    Processing helix  chain 'G' and resid 44 through 57
      removed outlier: 3.830A  pdb=" N   SER G  57 " --> pdb=" O   ARG G  53 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 63 through 76
    Processing helix  chain 'G' and resid 85 through 114
      removed outlier: 4.092A  pdb=" N   VAL G  89 " --> pdb=" O   GLN G  85 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 120 through 132
      removed outlier: 3.707A  pdb=" N   ILE G 124 " --> pdb=" O   MET G 120 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY G 132 " --> pdb=" O   ARG G 128 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 32 through 42
    Processing helix  chain 'H' and resid 49 through 77
      removed outlier: 4.732A  pdb=" N   ASP H  68 " --> pdb=" O   ASN H  64 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 82 through 94
      removed outlier: 3.836A  pdb=" N   VAL H  86 " --> pdb=" O   THR H  82 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 27 through 36
    Processing helix  chain 'I' and resid 46 through 73
      removed outlier: 3.938A  pdb=" N   LEU I  65 " --> pdb=" O   GLU I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 79 through 90
      removed outlier: 4.093A  pdb=" N   LEU I  83 " --> pdb=" O   ILE I  79 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP I  90 " --> pdb=" O   ALA I  86 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 91 through 97
    Processing helix  chain 'J' and resid 34 through 46
    Processing helix  chain 'J' and resid 52 through 81
      removed outlier: 3.670A  pdb=" N   MET J  56 " --> pdb=" O   SER J  52 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 87 through 99
      removed outlier: 3.904A  pdb=" N   ILE J  91 " --> pdb=" O   THR J  87 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 101 through 120
      removed outlier: 4.028A  pdb=" N   SER J 109 " --> pdb=" O   LYS J 105 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   SER J 120 " --> pdb=" O   THR J 116 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 44 through 57
      removed outlier: 3.833A  pdb=" N   SER K  57 " --> pdb=" O   ARG K  53 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 63 through 76
    Processing helix  chain 'K' and resid 85 through 114
      removed outlier: 4.096A  pdb=" N   VAL K  89 " --> pdb=" O   GLN K  85 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.707A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLY K 132 " --> pdb=" O   ARG K 128 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 25 through 29
      removed outlier: 3.549A  pdb=" N   GLY L  28 " --> pdb=" O   ASN L  25 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 25 through 29'
    Processing helix  chain 'L' and resid 30 through 42
      removed outlier: 3.767A  pdb=" N   ILE L  34 " --> pdb=" O   THR L  30 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 4.559A  pdb=" N   ASP L  68 " --> pdb=" O   ASN L  64 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 94
      removed outlier: 4.181A  pdb=" N   VAL L  86 " --> pdb=" O   THR L  82 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 16 through 22
    Processing helix  chain 'M' and resid 27 through 37
    Processing helix  chain 'M' and resid 46 through 73
      removed outlier: 4.024A  pdb=" N   ASN M  68 " --> pdb=" O   GLU M  64 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ALA M  69 " --> pdb=" O   LEU M  65 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 92 through 97
    Processing helix  chain 'N' and resid 34 through 46
      removed outlier: 3.535A  pdb=" N   VAL N  38 " --> pdb=" O   TYR N  34 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 52 through 81
      removed outlier: 3.811A  pdb=" N   MET N  56 " --> pdb=" O   SER N  52 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 99
    Processing helix  chain 'N' and resid 100 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32
      removed outlier: 3.755A  pdb=" N   THR A  31 " --> pdb=" O   ALA A  40 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A  40 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 115
      removed outlier: 3.906A  pdb=" N   LYS A 112 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   MET A 134 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 159
      removed outlier: 3.666A  pdb=" N   PHE A 189 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA A 187 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216
      removed outlier: 3.668A  pdb=" N   GLN A 243 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 259
      removed outlier: 3.849A  pdb=" N   LYS A 256 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   CYS A 258 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL A 267 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 266 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   TYR A 277 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 276 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS A 288 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 303
      removed outlier: 3.721A  pdb=" N   ASP A 300 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ILE A 310 " --> pdb=" O   TRP A 321 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TRP A 321 " --> pdb=" O   ILE A 310 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 312 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 317 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 40
      removed outlier: 7.500A  pdb=" N   LEU B 329 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER B 318 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TRP B 330 " --> pdb=" O   ILE B 316 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ILE B 316 " --> pdb=" O   TRP B 330 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER B 306 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 53
      removed outlier: 3.984A  pdb=" N   SER B  50 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER B  63 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS B  52 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA B  61 " --> pdb=" O   LYS B  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 70
    Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 93
      removed outlier: 3.899A  pdb=" N   ASP B  92 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 137
      removed outlier: 3.889A  pdb=" N   CYS B 134 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLY B 147 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ASN B 136 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 174 through 179
      removed outlier: 7.402A  pdb=" N   SER B 189 " --> pdb=" O   SER B 175 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   VAL B 177 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   VAL B 187 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   PHE B 179 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LEU B 185 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG B 196 " --> pdb=" O   SER B 188 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ILE B 197 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 228 through 231
      removed outlier: 3.583A  pdb=" N   ILE B 229 " --> pdb=" O   TRP B 241 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 276
      removed outlier: 3.608A  pdb=" N   TRP B 286 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU B 297 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 3834 through 3835
    Processing sheet with id=AB7, first strand: chain 'C' and resid 3856 through 3857
      removed outlier: 4.054A  pdb=" N   ILE C3856 " --> pdb=" O   ILE C3928 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL C3927 " --> pdb=" O   ARG C3916 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG C3916 " --> pdb=" O   VAL C3927 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 3862 through 3864
    Processing sheet with id=AB9, first strand: chain 'C' and resid 3919 through 3920
      removed outlier: 3.972A  pdb=" N   ILE C3920 " --> pdb=" O   GLN C3923 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 299 through 300
    Processing sheet with id=AC2, first strand: chain 'D' and resid 316 through 317
      removed outlier: 3.671A  pdb=" N   SER D 347 " --> pdb=" O   PHE D 469 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA D 471 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLY D 345 " --> pdb=" O   ALA D 471 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   SER D 473 " --> pdb=" O   ARG D 343 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG D 343 " --> pdb=" O   SER D 473 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 331 through 332
    Processing sheet with id=AC4, first strand: chain 'D' and resid 373 through 374
    Processing sheet with id=AC5, first strand: chain 'D' and resid 447 through 451
      removed outlier: 7.551A  pdb=" N   ILE D 447 " --> pdb=" O   ALA D 459 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLY D 457 " --> pdb=" O   PHE D 449 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LYS D 451 " --> pdb=" O   ASN D 455 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ASN D 455 " --> pdb=" O   LYS D 451 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'H' and resid 96 through 98
      removed outlier: 6.636A  pdb=" N   THR H  96 " --> pdb=" O   THR M 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'I' and resid 42 through 43
      removed outlier: 7.204A  pdb=" N   ARG I  42 " --> pdb=" O   ILE J  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.558A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC8
    Processing sheet with id=AC9, first strand: chain 'M' and resid 77 through 78
      removed outlier: 3.529A  pdb=" N   ILE M  78 " --> pdb=" O   GLY N  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9

    481 hydrogen bonds defined for protein.
    1395 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      358 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      238 stacking parallelities
  Total time for adding SS restraints: 4.14

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4080
        1.33 -     1.45: 5991
        1.45 -     1.57: 10009
        1.57 -     1.69: 580
        1.69 -     1.81: 83
  Bond restraints: 20743
  Sorted by residual:
  bond pdb=" CA  ILE C3861 "
       pdb=" CB  ILE C3861 "
    ideal  model  delta    sigma   weight residual
    1.533  1.583 -0.051 1.20e-02 6.94e+03 1.78e+01
  bond pdb=" CA  THR A 195 "
       pdb=" CB  THR A 195 "
    ideal  model  delta    sigma   weight residual
    1.530  1.577 -0.046 1.69e-02 3.50e+03 7.53e+00
  bond pdb=" C   ILE C3861 "
       pdb=" N   VAL C3862 "
    ideal  model  delta    sigma   weight residual
    1.332  1.307  0.025 9.20e-03 1.18e+04 7.29e+00
  bond pdb=" N   THR A 195 "
       pdb=" CA  THR A 195 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.29e-02 6.01e+03 6.34e+00
  bond pdb=" C3'  DT O  15 "
       pdb=" O3'  DT O  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 5.00e+00
  ... (remaining 20738 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 28198
        2.02 -     4.05: 973
        4.05 -     6.07: 77
        6.07 -     8.10: 22
        8.10 -    10.12: 4
  Bond angle restraints: 29274
  Sorted by residual:
  angle pdb=" N   THR A 195 "
        pdb=" CA  THR A 195 "
        pdb=" CB  THR A 195 "
      ideal   model   delta    sigma   weight residual
     110.49  120.61  -10.12 1.69e+00 3.50e-01 3.59e+01
  angle pdb=" N   ILE C3866 "
        pdb=" CA  ILE C3866 "
        pdb=" C   ILE C3866 "
      ideal   model   delta    sigma   weight residual
     113.47  108.37    5.10 1.01e+00 9.80e-01 2.55e+01
  angle pdb=" C   PRO A 107 "
        pdb=" N   SER A 108 "
        pdb=" CA  SER A 108 "
      ideal   model   delta    sigma   weight residual
     120.58  126.91   -6.33 1.32e+00 5.74e-01 2.30e+01
  angle pdb=" C   ASP H  24 "
        pdb=" N   ASN H  25 "
        pdb=" CA  ASN H  25 "
      ideal   model   delta    sigma   weight residual
     121.54  130.62   -9.08 1.91e+00 2.74e-01 2.26e+01
  angle pdb=" N   SER A 108 "
        pdb=" CA  SER A 108 "
        pdb=" C   SER A 108 "
      ideal   model   delta    sigma   weight residual
     113.45  119.31   -5.86 1.39e+00 5.18e-01 1.78e+01
  ... (remaining 29269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.21: 10232
       34.21 -    68.42: 1422
       68.42 -   102.63: 26
      102.63 -   136.84: 1
      136.84 -   171.05: 3
  Dihedral angle restraints: 11684
    sinusoidal: 6623
      harmonic: 5061
  Sorted by residual:
  dihedral pdb=" CA  LYS H  31 "
           pdb=" C   LYS H  31 "
           pdb=" N   PRO H  32 "
           pdb=" CA  PRO H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.55   45.45     0      5.00e+00 4.00e-02 8.26e+01
  dihedral pdb=" N   THR A 195 "
           pdb=" C   THR A 195 "
           pdb=" CA  THR A 195 "
           pdb=" CB  THR A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  144.12  -20.72     0      2.50e+00 1.60e-01 6.87e+01
  dihedral pdb=" C   THR A 195 "
           pdb=" N   THR A 195 "
           pdb=" CA  THR A 195 "
           pdb=" CB  THR A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -140.79   18.79     0      2.50e+00 1.60e-01 5.65e+01
  ... (remaining 11681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 3261
       0.151 -    0.302: 23
       0.302 -    0.452: 0
       0.452 -    0.603: 0
       0.603 -    0.754: 1
  Chirality restraints: 3285
  Sorted by residual:
  chirality pdb=" CA  THR A 195 "
            pdb=" N   THR A 195 "
            pdb=" C   THR A 195 "
            pdb=" CB  THR A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.77    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  SER A 108 "
            pdb=" N   SER A 108 "
            pdb=" C   SER A 108 "
            pdb=" CB  SER A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  LEU G  65 "
            pdb=" N   LEU G  65 "
            pdb=" C   LEU G  65 "
            pdb=" CB  LEU G  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 3282 not shown)

  Planarity restraints: 2701
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  31 "    0.072 5.00e-02 4.00e+02   1.10e-01 1.95e+01
        pdb=" N   PRO H  32 "   -0.191 5.00e-02 4.00e+02
        pdb=" CA  PRO H  32 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO H  32 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 223 "    0.043 5.00e-02 4.00e+02   6.46e-02 6.67e+00
        pdb=" N   PRO B 224 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 224 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 224 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 126 "    0.042 5.00e-02 4.00e+02   6.35e-02 6.45e+00
        pdb=" N   PRO A 127 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 127 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 127 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2698 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.19: 17
        2.19 -     2.87: 6208
        2.87 -     3.55: 26361
        3.55 -     4.22: 47280
        4.22 -     4.90: 73348
  Nonbonded interactions: 153214
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 332 "
            pdb=" OG1 THR B 208 "
     model   vdw
     1.513 3.040
  nonbonded pdb=" CG  PRO A 334 "
            pdb=" O   THR B 208 "
     model   vdw
     1.669 3.440
  nonbonded pdb=" O   PHE A 332 "
            pdb=" CB  THR B 208 "
     model   vdw
     1.695 3.470
  nonbonded pdb=" C   PHE A 332 "
            pdb=" OG1 THR B 208 "
     model   vdw
     1.723 3.270
  nonbonded pdb=" O   PHE A 332 "
            pdb=" CG2 THR B 208 "
     model   vdw
     1.771 3.460
  ... (remaining 153209 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 'G'
  selection = chain 'K'
}
ncs_group {
  reference = (chain 'H' and resid 24 through 101)
  selection = chain 'L'
}
ncs_group {
  reference = (chain 'I' and resid 13 through 117)
  selection = chain 'M'
}
ncs_group {
  reference = (chain 'J' and resid 28 through 120)
  selection = (chain 'N' and resid 28 through 120)
}

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=1.00 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:             3.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.660
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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      :  0.006   0.068  20743  Z= 0.271
  Angle     :  0.844  10.121  29274  Z= 0.487
  Chirality :  0.052   0.754   3285
  Planarity :  0.007   0.110   2701
  Dihedral  : 22.769 171.047   8424
  Min Nonbonded Distance : 1.513

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.82 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.74 (0.17), residues: 1717
  helix: -1.12 (0.18), residues: 556
  sheet: -3.15 (0.28), residues: 246
  loop : -3.27 (0.16), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C3765 
 TYR   0.034   0.003   TYR H  51 
 PHE   0.017   0.002   PHE A 213 
 TRP   0.024   0.003   TRP A  51 
 HIS   0.011   0.002   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (20743)
  covalent geometry    : angle       0.84367 (29274)
  hydrogen bonds       : bond        0.18191 (  839)
  hydrogen bonds       : angle       5.46859 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  567 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 566
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 ASP cc_start: 0.7250 (t0) cc_final: 0.6943 (p0)
REVERT: A  245 LEU cc_start: 0.9036 (mt) cc_final: 0.8601 (mt)
REVERT: A  248 LEU cc_start: 0.8950 (mt) cc_final: 0.8637 (mt)
REVERT: A  250 ASN cc_start: 0.9051 (m-40) cc_final: 0.8544 (p0)
REVERT: A  262 ASP cc_start: 0.8125 (p0) cc_final: 0.7768 (p0)
REVERT: A  277 TYR cc_start: 0.8073 (m-10) cc_final: 0.7280 (m-80)
REVERT: B   53 PHE cc_start: 0.1419 (m-80) cc_final: 0.1178 (p90)
REVERT: B  252 TYR cc_start: 0.4022 (m-80) cc_final: 0.2872 (t80)
REVERT: C 3823 LEU cc_start: 0.8217 (tp) cc_final: 0.7208 (tp)
REVERT: C 3844 PHE cc_start: 0.7844 (m-80) cc_final: 0.7450 (m-80)
REVERT: C 3855 VAL cc_start: 0.8449 (t) cc_final: 0.7683 (p)
REVERT: C 3867 LEU cc_start: 0.8357 (tp) cc_final: 0.8140 (tp)
REVERT: C 3871 ARG cc_start: 0.8453 (mtt-85) cc_final: 0.8209 (mmp-170)
REVERT: D  315 MET cc_start: 0.5782 (ttp) cc_final: 0.5146 (ppp)
REVERT: D  338 PRO cc_start: 0.6609 (Cg_exo) cc_final: 0.6399 (Cg_endo)
REVERT: D  397 ASN cc_start: 0.6647 (t0) cc_final: 0.6358 (t0)
REVERT: D  448 ILE cc_start: 0.6713 (mt) cc_final: 0.5891 (mp)
REVERT: D  500 MET cc_start: 0.1472 (mmm) cc_final: 0.1176 (mtm)
REVERT: G   48 LEU cc_start: 0.9220 (mt) cc_final: 0.8986 (mm)
REVERT: G   62 ILE cc_start: 0.9001 (mt) cc_final: 0.8736 (mm)
REVERT: G   64 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8556 (mmmm)
REVERT: G   65 LEU cc_start: 0.9294 (mp) cc_final: 0.8930 (mm)
REVERT: G   68 GLN cc_start: 0.9396 (tt0) cc_final: 0.9119 (pt0)
REVERT: G   76 GLN cc_start: 0.8480 (tt0) cc_final: 0.7671 (tp-100)
REVERT: G   89 VAL cc_start: 0.9776 (t) cc_final: 0.9470 (t)
REVERT: G   99 TYR cc_start: 0.9094 (t80) cc_final: 0.8649 (t80)
REVERT: G  105 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8425 (mm-30)
REVERT: G  107 THR cc_start: 0.9726 (m) cc_final: 0.9511 (p)
REVERT: G  120 MET cc_start: 0.6823 (mtt) cc_final: 0.6388 (mtp)
REVERT: H   49 LEU cc_start: 0.9499 (mt) cc_final: 0.9163 (mt)
REVERT: H   64 ASN cc_start: 0.9245 (m-40) cc_final: 0.8951 (t0)
REVERT: H   67 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8411 (tpp-160)
REVERT: H   75 HIS cc_start: 0.8717 (t70) cc_final: 0.7912 (t-170)
REVERT: H   79 LYS cc_start: 0.8568 (mttt) cc_final: 0.8237 (ptpp)
REVERT: H   93 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8899 (tp40)
REVERT: H   97 LEU cc_start: 0.9490 (tp) cc_final: 0.9169 (mm)
REVERT: H   98 TYR cc_start: 0.8106 (m-10) cc_final: 0.7261 (m-80)
REVERT: I   56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8337 (tm-30)
REVERT: I   72 ASP cc_start: 0.8213 (m-30) cc_final: 0.8002 (p0)
REVERT: I   73 ASN cc_start: 0.8854 (m-40) cc_final: 0.8640 (p0)
REVERT: I   81 ARG cc_start: 0.9289 (tpt-90) cc_final: 0.8906 (tpt170)
REVERT: I   85 LEU cc_start: 0.9471 (mt) cc_final: 0.9191 (mm)
REVERT: I   89 ASN cc_start: 0.9545 (m-40) cc_final: 0.9176 (m110)
REVERT: I   90 ASP cc_start: 0.9163 (t0) cc_final: 0.8910 (p0)
REVERT: J   43 LYS cc_start: 0.9102 (mmtp) cc_final: 0.8800 (mmtm)
REVERT: J   54 LYS cc_start: 0.9591 (mmmt) cc_final: 0.9357 (mmmt)
REVERT: J   59 MET cc_start: 0.9471 (mmm) cc_final: 0.9114 (mmm)
REVERT: J   65 ASP cc_start: 0.9270 (t0) cc_final: 0.9067 (t0)
REVERT: J   76 ARG cc_start: 0.9379 (ttm110) cc_final: 0.8901 (ttm110)
REVERT: J   77 LEU cc_start: 0.9352 (mt) cc_final: 0.8747 (mt)
REVERT: J   85 THR cc_start: 0.9039 (m) cc_final: 0.8722 (p)
REVERT: J   96 ARG cc_start: 0.9286 (ttm170) cc_final: 0.9038 (ttm170)
REVERT: K   48 LEU cc_start: 0.8928 (mt) cc_final: 0.8283 (mm)
REVERT: K  100 LEU cc_start: 0.9790 (mt) cc_final: 0.9458 (pp)
REVERT: L   27 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8438 (mp10)
REVERT: L   53 GLU cc_start: 0.9436 (tp30) cc_final: 0.9048 (tt0)
REVERT: L   63 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8170 (mm-30)
REVERT: L   66 ILE cc_start: 0.9211 (mt) cc_final: 0.8831 (pt)
REVERT: L   91 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8648 (tptm)
REVERT: M   61 GLU cc_start: 0.9448 (tp30) cc_final: 0.8963 (tm-30)
REVERT: M   88 ARG cc_start: 0.9403 (mmt-90) cc_final: 0.9172 (mmt180)
REVERT: N   40 LYS cc_start: 0.9453 (mttt) cc_final: 0.9171 (mttt)
REVERT: N   59 MET cc_start: 0.9478 (mmm) cc_final: 0.9081 (mmm)
REVERT: N   65 ASP cc_start: 0.8939 (t0) cc_final: 0.8672 (t0)
REVERT: N   68 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8764 (mm-30)
REVERT: N   69 ARG cc_start: 0.9489 (ttm110) cc_final: 0.9036 (ttm110)
REVERT: N   82 LYS cc_start: 0.9673 (mttt) cc_final: 0.9339 (tptt)
REVERT: N   87 THR cc_start: 0.7521 (p) cc_final: 0.6417 (p)
REVERT: N   90 GLU cc_start: 0.9231 (mp0) cc_final: 0.8520 (mp0)
REVERT: N   92 GLN cc_start: 0.9102 (tt0) cc_final: 0.8842 (mt0)
REVERT: N   98 LEU cc_start: 0.9539 (tp) cc_final: 0.9214 (tp)
REVERT: N  113 LYS cc_start: 0.8985 (ttpp) cc_final: 0.8780 (ttmm)
REVERT: N  116 THR cc_start: 0.9573 (m) cc_final: 0.9342 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 567
  average time/residue: 0.1920
  time to fit residues: 151.4393
Evaluate side-chains
  289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 288
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 194 optimal weight:    4.9990
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  65 HIS
A  88 ASN
A 323 GLN
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 320 HIS
D 354 GLN
D 381 HIS
** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN
G 125 GLN
I  31 HIS
I  73 ASN
** J  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  64 ASN
** N  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.092349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.065861 restraints weight = 107857.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.067712 restraints weight = 59940.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.068924 restraints weight = 39782.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.069616 restraints weight = 29844.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.070152 restraints weight = 24788.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  20743  Z= 0.152
  Angle     :  0.613   9.385  29274  Z= 0.347
  Chirality :  0.040   0.278   3285
  Planarity :  0.005   0.089   2701
  Dihedral  : 27.307 172.552   5080
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.15 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.19), residues: 1717
  helix:  0.46 (0.21), residues: 564
  sheet: -2.61 (0.30), residues: 260
  loop : -2.92 (0.17), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  42 
 TYR   0.019   0.001   TYR C3942 
 PHE   0.010   0.001   PHE A 189 
 TRP   0.016   0.002   TRP D 327 
 HIS   0.009   0.001   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (20743)
  covalent geometry    : angle       0.61285 (29274)
  hydrogen bonds       : bond        0.05038 (  839)
  hydrogen bonds       : angle       3.86756 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  400 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 396
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 MET cc_start: 0.4911 (tpp) cc_final: 0.4650 (tpp)
REVERT: A  142 HIS cc_start: 0.6875 (p90) cc_final: 0.6508 (p-80)
REVERT: A  148 ASP cc_start: 0.7181 (t0) cc_final: 0.6933 (p0)
REVERT: A  184 ASP cc_start: 0.8538 (t0) cc_final: 0.8210 (t0)
REVERT: A  250 ASN cc_start: 0.9398 (m-40) cc_final: 0.8887 (p0)
REVERT: A  273 GLN cc_start: 0.7840 (mt0) cc_final: 0.7622 (pm20)
REVERT: A  276 LEU cc_start: 0.8480 (mt) cc_final: 0.7940 (tp)
REVERT: A  277 TYR cc_start: 0.8170 (m-10) cc_final: 0.7472 (m-80)
REVERT: A  279 TRP cc_start: 0.8468 (m-90) cc_final: 0.7787 (m-90)
REVERT: B   53 PHE cc_start: 0.1968 (m-80) cc_final: 0.1362 (p90)
REVERT: B  252 TYR cc_start: 0.4297 (m-80) cc_final: 0.2837 (t80)
REVERT: C 3844 PHE cc_start: 0.8249 (m-80) cc_final: 0.8023 (m-80)
REVERT: C 3867 LEU cc_start: 0.8542 (tp) cc_final: 0.8180 (tp)
REVERT: C 3871 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8213 (mmp-170)
REVERT: C 3897 MET cc_start: 0.4770 (ttm) cc_final: 0.4338 (ptp)
REVERT: C 3942 TYR cc_start: 0.7117 (t80) cc_final: 0.6342 (t80)
REVERT: D  315 MET cc_start: 0.5954 (ttp) cc_final: 0.5464 (ppp)
REVERT: D  336 MET cc_start: 0.2171 (tmm) cc_final: 0.1958 (tmm)
REVERT: D  397 ASN cc_start: 0.6839 (t0) cc_final: 0.6544 (t0)
REVERT: D  500 MET cc_start: 0.1454 (mmm) cc_final: 0.1153 (mtm)
REVERT: G   50 GLU cc_start: 0.9405 (tp30) cc_final: 0.8736 (tm-30)
REVERT: G   60 LEU cc_start: 0.7800 (pt) cc_final: 0.7527 (pt)
REVERT: G   65 LEU cc_start: 0.9412 (mp) cc_final: 0.8395 (mt)
REVERT: G   67 PHE cc_start: 0.9274 (t80) cc_final: 0.8874 (t80)
REVERT: G   76 GLN cc_start: 0.8417 (tt0) cc_final: 0.7661 (tp-100)
REVERT: G   93 GLN cc_start: 0.9220 (mt0) cc_final: 0.8881 (mt0)
REVERT: G   99 TYR cc_start: 0.8879 (t80) cc_final: 0.8634 (t80)
REVERT: G  105 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8505 (mm-30)
REVERT: G  119 ILE cc_start: 0.8138 (mt) cc_final: 0.7772 (mt)
REVERT: G  120 MET cc_start: 0.7308 (mtt) cc_final: 0.6753 (mtm)
REVERT: H   44 LYS cc_start: 0.8672 (tppp) cc_final: 0.8044 (tppt)
REVERT: H   67 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8339 (ttm-80)
REVERT: H   75 HIS cc_start: 0.8800 (t70) cc_final: 0.8454 (t70)
REVERT: H   79 LYS cc_start: 0.8833 (mttt) cc_final: 0.8257 (ptpp)
REVERT: H   92 ARG cc_start: 0.9356 (mtp-110) cc_final: 0.8968 (ttt180)
REVERT: H   93 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8892 (tp40)
REVERT: H   97 LEU cc_start: 0.9564 (tp) cc_final: 0.9287 (mm)
REVERT: H   98 TYR cc_start: 0.8955 (m-10) cc_final: 0.8123 (m-80)
REVERT: I   13 LYS cc_start: 0.6142 (tptp) cc_final: 0.5932 (tptt)
REVERT: I   23 LEU cc_start: 0.9230 (mm) cc_final: 0.8944 (mm)
REVERT: I   38 ASN cc_start: 0.7121 (t0) cc_final: 0.6817 (t0)
REVERT: I   56 GLU cc_start: 0.8881 (tt0) cc_final: 0.8382 (tm-30)
REVERT: I  104 GLN cc_start: 0.8485 (mp10) cc_final: 0.8039 (mp10)
REVERT: J   54 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9234 (mmmt)
REVERT: J   76 ARG cc_start: 0.9377 (ttm110) cc_final: 0.9051 (ttm110)
REVERT: J   96 ARG cc_start: 0.9319 (ttm170) cc_final: 0.8996 (ttm170)
REVERT: K   71 VAL cc_start: 0.9614 (m) cc_final: 0.9369 (p)
REVERT: K   77 ASP cc_start: 0.8666 (m-30) cc_final: 0.8204 (p0)
REVERT: K   84 PHE cc_start: 0.8476 (m-80) cc_final: 0.8179 (m-10)
REVERT: K  106 ASP cc_start: 0.7604 (m-30) cc_final: 0.7399 (m-30)
REVERT: L   25 ASN cc_start: 0.8247 (m-40) cc_final: 0.8018 (m-40)
REVERT: L   44 LYS cc_start: 0.9081 (mttm) cc_final: 0.8802 (mttt)
REVERT: L   68 ASP cc_start: 0.9082 (m-30) cc_final: 0.8845 (p0)
REVERT: L   88 TYR cc_start: 0.9366 (m-10) cc_final: 0.8737 (m-80)
REVERT: M   83 LEU cc_start: 0.9490 (mt) cc_final: 0.9221 (mm)
REVERT: N   40 LYS cc_start: 0.9654 (mttt) cc_final: 0.9127 (mtmm)
REVERT: N   56 MET cc_start: 0.8875 (tpp) cc_final: 0.8673 (tpp)
REVERT: N   59 MET cc_start: 0.9260 (mmm) cc_final: 0.8879 (mmp)
REVERT: N   69 ARG cc_start: 0.9263 (ttm110) cc_final: 0.9023 (ttm110)
REVERT: N   73 GLU cc_start: 0.8830 (tp30) cc_final: 0.8606 (tp30)
REVERT: N   82 LYS cc_start: 0.9536 (mttt) cc_final: 0.9236 (tppt)
REVERT: N   90 GLU cc_start: 0.9213 (mp0) cc_final: 0.8856 (mp0)
REVERT: N  116 THR cc_start: 0.9529 (m) cc_final: 0.9310 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 399
  average time/residue: 0.1550
  time to fit residues: 91.3358
Evaluate side-chains
  274 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 273
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 123 optimal weight:    8.9990
   chunk 76 optimal weight:    4.9990
   chunk 6 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 143 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 110 optimal weight:    4.9990
   chunk 151 optimal weight:    0.0980
   chunk 161 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9980
   chunk 146 optimal weight:    0.8980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 285 ASN
B  86 HIS
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 376 GLN
** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  46 HIS
N  81 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.086970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.061022 restraints weight = 111060.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.062791 restraints weight = 62318.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.063964 restraints weight = 41537.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.064771 restraints weight = 31103.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.065244 restraints weight = 25464.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  20743  Z= 0.162
  Angle     :  0.589   8.398  29274  Z= 0.334
  Chirality :  0.039   0.241   3285
  Planarity :  0.005   0.090   2701
  Dihedral  : 26.969 175.198   5080
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.42 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.19), residues: 1717
  helix:  1.10 (0.22), residues: 566
  sheet: -2.17 (0.29), residues: 275
  loop : -2.71 (0.18), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 118 
 TYR   0.014   0.001   TYR H  51 
 PHE   0.018   0.001   PHE G 104 
 TRP   0.018   0.002   TRP D 327 
 HIS   0.009   0.001   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (20743)
  covalent geometry    : angle       0.58870 (29274)
  hydrogen bonds       : bond        0.04615 (  839)
  hydrogen bonds       : angle       3.58965 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 359
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 ASP cc_start: 0.7410 (t0) cc_final: 0.7140 (p0)
REVERT: A  184 ASP cc_start: 0.8598 (t0) cc_final: 0.8282 (t0)
REVERT: A  215 ILE cc_start: 0.9225 (pt) cc_final: 0.8992 (pt)
REVERT: A  250 ASN cc_start: 0.9549 (m-40) cc_final: 0.8650 (t0)
REVERT: A  257 CYS cc_start: 0.8643 (m) cc_final: 0.8126 (t)
REVERT: A  273 GLN cc_start: 0.7943 (mt0) cc_final: 0.7545 (pm20)
REVERT: A  276 LEU cc_start: 0.8552 (mt) cc_final: 0.7983 (tp)
REVERT: A  277 TYR cc_start: 0.8194 (m-10) cc_final: 0.7589 (m-80)
REVERT: A  279 TRP cc_start: 0.8640 (m-90) cc_final: 0.7579 (m-90)
REVERT: B   53 PHE cc_start: 0.1791 (m-80) cc_final: 0.1042 (p90)
REVERT: C 3818 MET cc_start: 0.8886 (mtm) cc_final: 0.8609 (mtm)
REVERT: C 3856 ILE cc_start: 0.7249 (tp) cc_final: 0.6866 (tp)
REVERT: C 3867 LEU cc_start: 0.8696 (tp) cc_final: 0.7987 (tp)
REVERT: C 3871 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.7807 (mmp-170)
REVERT: C 3897 MET cc_start: 0.5057 (ttm) cc_final: 0.4619 (ptp)
REVERT: C 3932 ARG cc_start: 0.8616 (mpp-170) cc_final: 0.7965 (ppt170)
REVERT: D  315 MET cc_start: 0.6250 (ttp) cc_final: 0.5658 (ppp)
REVERT: D  336 MET cc_start: 0.2208 (tmm) cc_final: 0.1942 (tmm)
REVERT: D  397 ASN cc_start: 0.6840 (t0) cc_final: 0.6551 (t0)
REVERT: D  500 MET cc_start: 0.1194 (mmm) cc_final: 0.0992 (mtm)
REVERT: G   50 GLU cc_start: 0.9376 (tp30) cc_final: 0.8727 (tm-30)
REVERT: G   56 LYS cc_start: 0.8728 (tppp) cc_final: 0.8476 (tppp)
REVERT: G   65 LEU cc_start: 0.9152 (mp) cc_final: 0.8756 (mt)
REVERT: G   67 PHE cc_start: 0.9372 (t80) cc_final: 0.9117 (t80)
REVERT: G   76 GLN cc_start: 0.8536 (tt0) cc_final: 0.7672 (tp-100)
REVERT: G   93 GLN cc_start: 0.9373 (mt0) cc_final: 0.8650 (mt0)
REVERT: G   97 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8812 (mm-30)
REVERT: G  105 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8628 (tp30)
REVERT: G  120 MET cc_start: 0.6791 (mtt) cc_final: 0.6226 (mtm)
REVERT: H   75 HIS cc_start: 0.8741 (t70) cc_final: 0.8412 (t70)
REVERT: H   79 LYS cc_start: 0.9016 (mttt) cc_final: 0.8439 (ptpp)
REVERT: H   88 TYR cc_start: 0.9159 (m-10) cc_final: 0.8822 (m-80)
REVERT: H   92 ARG cc_start: 0.9416 (mtp-110) cc_final: 0.9061 (ttt180)
REVERT: H   97 LEU cc_start: 0.9616 (tp) cc_final: 0.9305 (mm)
REVERT: I   23 LEU cc_start: 0.9263 (mm) cc_final: 0.8957 (mm)
REVERT: I   38 ASN cc_start: 0.7241 (t0) cc_final: 0.6504 (t0)
REVERT: I   51 LEU cc_start: 0.9496 (tp) cc_final: 0.9161 (tp)
REVERT: I   55 LEU cc_start: 0.9705 (mm) cc_final: 0.9484 (mm)
REVERT: I   56 GLU cc_start: 0.8925 (tt0) cc_final: 0.8482 (tm-30)
REVERT: I   64 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8855 (tm-30)
REVERT: I   72 ASP cc_start: 0.8099 (p0) cc_final: 0.7845 (p0)
REVERT: I   74 LYS cc_start: 0.9136 (tttp) cc_final: 0.8469 (tptp)
REVERT: J   32 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8585 (tp30)
REVERT: J   95 VAL cc_start: 0.9511 (t) cc_final: 0.9278 (p)
REVERT: J   96 ARG cc_start: 0.9346 (ttm170) cc_final: 0.8961 (ttm170)
REVERT: K   59 GLU cc_start: 0.7610 (mp0) cc_final: 0.7404 (mp0)
REVERT: K   68 GLN cc_start: 0.9512 (pt0) cc_final: 0.9272 (pt0)
REVERT: K   71 VAL cc_start: 0.9743 (m) cc_final: 0.9516 (p)
REVERT: K   76 GLN cc_start: 0.9174 (tt0) cc_final: 0.8208 (tp-100)
REVERT: K   77 ASP cc_start: 0.8957 (m-30) cc_final: 0.8544 (p0)
REVERT: K   84 PHE cc_start: 0.8642 (m-80) cc_final: 0.8302 (m-10)
REVERT: K   94 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9126 (mm-30)
REVERT: K   97 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8901 (mt-10)
REVERT: K  120 MET cc_start: 0.8417 (mmm) cc_final: 0.8166 (mmp)
REVERT: L   44 LYS cc_start: 0.9321 (mttm) cc_final: 0.8947 (mttt)
REVERT: L   63 GLU cc_start: 0.8856 (pp20) cc_final: 0.8154 (mt-10)
REVERT: L   68 ASP cc_start: 0.9365 (m-30) cc_final: 0.8979 (p0)
REVERT: L   88 TYR cc_start: 0.9489 (m-10) cc_final: 0.8955 (m-80)
REVERT: M   38 ASN cc_start: 0.8734 (p0) cc_final: 0.7980 (p0)
REVERT: M   61 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8876 (tm-30)
REVERT: M   64 GLU cc_start: 0.8994 (tp30) cc_final: 0.8333 (mm-30)
REVERT: M   83 LEU cc_start: 0.9544 (mt) cc_final: 0.9333 (mm)
REVERT: N   40 LYS cc_start: 0.9670 (mttt) cc_final: 0.9297 (mmtt)
REVERT: N   59 MET cc_start: 0.9209 (mmm) cc_final: 0.8880 (mmp)
REVERT: N   69 ARG cc_start: 0.9089 (ttm110) cc_final: 0.8758 (ttm110)
REVERT: N   73 GLU cc_start: 0.9100 (tp30) cc_final: 0.8816 (tp30)
REVERT: N   90 GLU cc_start: 0.9165 (mp0) cc_final: 0.8801 (mp0)
REVERT: N   92 GLN cc_start: 0.8896 (mt0) cc_final: 0.8370 (mt0)
REVERT: N  113 LYS cc_start: 0.9531 (ttmm) cc_final: 0.9289 (ttmm)
REVERT: N  116 THR cc_start: 0.9499 (m) cc_final: 0.9254 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 361
  average time/residue: 0.1580
  time to fit residues: 83.5222
Evaluate side-chains
  269 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 138 optimal weight:    4.9990
   chunk 117 optimal weight:    5.9990
   chunk 165 optimal weight:    0.7980
   chunk 127 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 184 optimal weight:    5.9990
   chunk 28 optimal weight:   20.0000
   chunk 40 optimal weight:   40.0000
   chunk 173 optimal weight:    4.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  65 HIS
A  92 GLN
A 120 GLN
A 154 ASN
A 274 HIS
A 285 ASN
A 342 ASN
** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN
M  31 HIS
M  94 ASN
N  79 HIS
N  81 ASN
N 106 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.075864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.050518 restraints weight = 118152.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.052131 restraints weight = 65121.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.053229 restraints weight = 42950.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.053941 restraints weight = 32299.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.054433 restraints weight = 26566.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.6900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  20743  Z= 0.259
  Angle     :  0.705   8.895  29274  Z= 0.398
  Chirality :  0.043   0.252   3285
  Planarity :  0.006   0.087   2701
  Dihedral  : 27.263 174.473   5080
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.77 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.19), residues: 1717
  helix:  0.80 (0.21), residues: 559
  sheet: -2.24 (0.29), residues: 289
  loop : -2.47 (0.19), residues: 869

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG N  30 
 TYR   0.020   0.002   TYR H  51 
 PHE   0.023   0.002   PHE H  61 
 TRP   0.017   0.002   TRP D 327 
 HIS   0.010   0.002   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (20743)
  covalent geometry    : angle       0.70545 (29274)
  hydrogen bonds       : bond        0.07148 (  839)
  hydrogen bonds       : angle       4.15109 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 315
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 LEU cc_start: 0.8830 (mt) cc_final: 0.8558 (tt)
REVERT: A  250 ASN cc_start: 0.9661 (m-40) cc_final: 0.8736 (t0)
REVERT: A  258 CYS cc_start: 0.7095 (p) cc_final: 0.6865 (m)
REVERT: A  273 GLN cc_start: 0.8303 (mt0) cc_final: 0.7584 (pm20)
REVERT: A  280 GLU cc_start: 0.8134 (tt0) cc_final: 0.7923 (tt0)
REVERT: C 3784 LYS cc_start: 0.3747 (ttmm) cc_final: 0.3365 (pttp)
REVERT: C 3818 MET cc_start: 0.8860 (mtm) cc_final: 0.8605 (mtm)
REVERT: C 3867 LEU cc_start: 0.8670 (tp) cc_final: 0.8342 (tp)
REVERT: C 3897 MET cc_start: 0.5313 (ttm) cc_final: 0.4791 (ptm)
REVERT: C 3932 ARG cc_start: 0.8681 (mpp-170) cc_final: 0.8154 (ppt170)
REVERT: D  315 MET cc_start: 0.6571 (ttp) cc_final: 0.5850 (ttp)
REVERT: D  327 TRP cc_start: 0.5879 (m-90) cc_final: 0.5212 (m-90)
REVERT: D  336 MET cc_start: 0.2263 (tmm) cc_final: 0.1994 (tmm)
REVERT: D  397 ASN cc_start: 0.6641 (t0) cc_final: 0.6389 (t0)
REVERT: G   50 GLU cc_start: 0.9349 (tp30) cc_final: 0.8691 (tm-30)
REVERT: G   56 LYS cc_start: 0.8871 (tppp) cc_final: 0.8524 (tppp)
REVERT: G   76 GLN cc_start: 0.8752 (tt0) cc_final: 0.8005 (tp-100)
REVERT: G   79 LYS cc_start: 0.8414 (tppp) cc_final: 0.8122 (tppt)
REVERT: G   89 VAL cc_start: 0.9845 (t) cc_final: 0.9489 (t)
REVERT: G   92 LEU cc_start: 0.9587 (mt) cc_final: 0.9375 (mt)
REVERT: G   93 GLN cc_start: 0.9386 (mt0) cc_final: 0.8597 (mt0)
REVERT: G   97 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8844 (mm-30)
REVERT: G  119 ILE cc_start: 0.7755 (mt) cc_final: 0.7398 (mt)
REVERT: G  120 MET cc_start: 0.7279 (mtt) cc_final: 0.6540 (mtm)
REVERT: H   53 GLU cc_start: 0.9531 (mp0) cc_final: 0.9020 (mp0)
REVERT: H   63 GLU cc_start: 0.8698 (pp20) cc_final: 0.8338 (tt0)
REVERT: H   79 LYS cc_start: 0.9273 (mttt) cc_final: 0.8714 (ptpp)
REVERT: H   84 MET cc_start: 0.9048 (mpp) cc_final: 0.8610 (mpp)
REVERT: H   88 TYR cc_start: 0.9270 (m-10) cc_final: 0.8847 (m-80)
REVERT: H   92 ARG cc_start: 0.9529 (mtp-110) cc_final: 0.9079 (ttt180)
REVERT: I   38 ASN cc_start: 0.7836 (t0) cc_final: 0.7550 (t0)
REVERT: I   56 GLU cc_start: 0.8671 (tt0) cc_final: 0.8354 (tm-30)
REVERT: I   64 GLU cc_start: 0.9291 (tm-30) cc_final: 0.9014 (tm-30)
REVERT: I   68 ASN cc_start: 0.9419 (t0) cc_final: 0.9098 (t0)
REVERT: I   74 LYS cc_start: 0.9173 (tttp) cc_final: 0.8552 (tptp)
REVERT: I   89 ASN cc_start: 0.9610 (m-40) cc_final: 0.9369 (m110)
REVERT: J   32 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8683 (tp30)
REVERT: J   59 MET cc_start: 0.9524 (mmp) cc_final: 0.9302 (mmm)
REVERT: J   61 SER cc_start: 0.9566 (m) cc_final: 0.9316 (p)
REVERT: J   62 PHE cc_start: 0.9588 (t80) cc_final: 0.9363 (t80)
REVERT: J   76 ARG cc_start: 0.9347 (ttm110) cc_final: 0.8928 (ttm110)
REVERT: J   77 LEU cc_start: 0.9552 (mt) cc_final: 0.9277 (mt)
REVERT: J   83 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.8135 (tpp80)
REVERT: J   90 GLU cc_start: 0.8723 (mp0) cc_final: 0.8135 (mp0)
REVERT: J   92 GLN cc_start: 0.9622 (tt0) cc_final: 0.9362 (tt0)
REVERT: J   96 ARG cc_start: 0.9453 (ttm170) cc_final: 0.9149 (ttm170)
REVERT: J  110 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8573 (tm-30)
REVERT: K   68 GLN cc_start: 0.9486 (pt0) cc_final: 0.9183 (pt0)
REVERT: K   76 GLN cc_start: 0.9208 (tt0) cc_final: 0.8830 (tp-100)
REVERT: K   79 LYS cc_start: 0.9056 (tptp) cc_final: 0.8804 (tppt)
REVERT: K   94 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9059 (mt-10)
REVERT: L   44 LYS cc_start: 0.9329 (mttm) cc_final: 0.9081 (mttt)
REVERT: L   51 TYR cc_start: 0.8104 (m-80) cc_final: 0.7861 (m-10)
REVERT: L   53 GLU cc_start: 0.9633 (tp30) cc_final: 0.9432 (tp30)
REVERT: L   63 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8434 (mt-10)
REVERT: L   68 ASP cc_start: 0.9474 (m-30) cc_final: 0.9154 (m-30)
REVERT: L   88 TYR cc_start: 0.9486 (m-10) cc_final: 0.9104 (m-80)
REVERT: M   38 ASN cc_start: 0.8945 (p0) cc_final: 0.8642 (p0)
REVERT: M   61 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: M   64 GLU cc_start: 0.9095 (tp30) cc_final: 0.8410 (mm-30)
REVERT: N   40 LYS cc_start: 0.9651 (mttt) cc_final: 0.9343 (mmtt)
REVERT: N   48 ASP cc_start: 0.8809 (p0) cc_final: 0.8343 (t0)
REVERT: N   59 MET cc_start: 0.9348 (mmm) cc_final: 0.8943 (mmm)
REVERT: N   73 GLU cc_start: 0.9315 (tp30) cc_final: 0.9113 (tp30)
REVERT: N   90 GLU cc_start: 0.9258 (mp0) cc_final: 0.8956 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 317
  average time/residue: 0.1520
  time to fit residues: 71.3871
Evaluate side-chains
  242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 143 optimal weight:    5.9990
   chunk 40 optimal weight:   40.0000
   chunk 70 optimal weight:    5.9990
   chunk 146 optimal weight:    0.9990
   chunk 171 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 57 optimal weight:   20.0000
   chunk 142 optimal weight:    5.9990
   chunk 132 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 8 optimal weight:   10.0000
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 323 GLN
B 323 ASN
** C3898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  89 ASN
** M  94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.075096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.050109 restraints weight = 119867.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.051794 restraints weight = 65376.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.052867 restraints weight = 42810.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.053600 restraints weight = 31927.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.054103 restraints weight = 26137.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.7783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  20743  Z= 0.208
  Angle     :  0.627   8.088  29274  Z= 0.355
  Chirality :  0.041   0.228   3285
  Planarity :  0.005   0.093   2701
  Dihedral  : 27.125 177.029   5080
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.22 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.19), residues: 1717
  helix:  1.08 (0.21), residues: 560
  sheet: -2.03 (0.30), residues: 274
  loop : -2.34 (0.19), residues: 883

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG N  30 
 TYR   0.015   0.002   TYR N  80 
 PHE   0.021   0.002   PHE K 104 
 TRP   0.013   0.001   TRP D 327 
 HIS   0.016   0.001   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (20743)
  covalent geometry    : angle       0.62670 (29274)
  hydrogen bonds       : bond        0.05444 (  839)
  hydrogen bonds       : angle       3.79607 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 308
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9664 (m-40) cc_final: 0.8798 (t0)
REVERT: A  273 GLN cc_start: 0.8518 (mt0) cc_final: 0.7816 (pm20)
REVERT: C 3779 ASN cc_start: 0.4383 (t0) cc_final: 0.3229 (p0)
REVERT: C 3784 LYS cc_start: 0.3621 (ttmm) cc_final: 0.2919 (pttp)
REVERT: C 3818 MET cc_start: 0.9005 (mtm) cc_final: 0.8571 (mtm)
REVERT: C 3897 MET cc_start: 0.4946 (ttm) cc_final: 0.4543 (ttp)
REVERT: D  315 MET cc_start: 0.6393 (ttp) cc_final: 0.5626 (ttp)
REVERT: D  329 PHE cc_start: 0.6203 (p90) cc_final: 0.5966 (p90)
REVERT: D  336 MET cc_start: 0.2364 (tmm) cc_final: 0.2077 (tmm)
REVERT: G   50 GLU cc_start: 0.9304 (tp30) cc_final: 0.8663 (tm-30)
REVERT: G   56 LYS cc_start: 0.8922 (tppp) cc_final: 0.8626 (tppp)
REVERT: G   76 GLN cc_start: 0.8885 (tt0) cc_final: 0.8259 (tp-100)
REVERT: G   93 GLN cc_start: 0.9373 (mt0) cc_final: 0.8834 (mt0)
REVERT: G  103 LEU cc_start: 0.9490 (tp) cc_final: 0.9267 (tp)
REVERT: G  119 ILE cc_start: 0.7572 (mt) cc_final: 0.7284 (mt)
REVERT: H   79 LYS cc_start: 0.9278 (mttt) cc_final: 0.8715 (mtmm)
REVERT: H   84 MET cc_start: 0.9013 (mpp) cc_final: 0.8643 (mpp)
REVERT: H   88 TYR cc_start: 0.9270 (m-10) cc_final: 0.8820 (m-80)
REVERT: H   92 ARG cc_start: 0.9436 (mtp-110) cc_final: 0.9028 (ttp80)
REVERT: I   13 LYS cc_start: 0.5967 (tppt) cc_final: 0.5756 (tppt)
REVERT: I   38 ASN cc_start: 0.7975 (t0) cc_final: 0.7610 (t0)
REVERT: I   56 GLU cc_start: 0.8621 (tt0) cc_final: 0.8266 (tm-30)
REVERT: I   64 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9017 (tm-30)
REVERT: I   68 ASN cc_start: 0.9488 (t0) cc_final: 0.9201 (t0)
REVERT: I   74 LYS cc_start: 0.9171 (tttp) cc_final: 0.8603 (tptp)
REVERT: I   89 ASN cc_start: 0.9624 (m-40) cc_final: 0.9292 (m110)
REVERT: J   32 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8873 (mm-30)
REVERT: J   76 ARG cc_start: 0.9412 (ttm110) cc_final: 0.9091 (ttm110)
REVERT: J   77 LEU cc_start: 0.9301 (mt) cc_final: 0.8987 (mt)
REVERT: J   83 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8477 (tpp80)
REVERT: K   68 GLN cc_start: 0.9473 (pt0) cc_final: 0.9166 (pt0)
REVERT: K   76 GLN cc_start: 0.9212 (tt0) cc_final: 0.8914 (tp-100)
REVERT: K   94 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9168 (mt-10)
REVERT: L   44 LYS cc_start: 0.9412 (mttm) cc_final: 0.9091 (mttt)
REVERT: L   50 ILE cc_start: 0.6434 (mm) cc_final: 0.6179 (mm)
REVERT: L   53 GLU cc_start: 0.9604 (tp30) cc_final: 0.9233 (tp30)
REVERT: L   59 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8059 (ttmt)
REVERT: L   63 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8385 (mt-10)
REVERT: L   68 ASP cc_start: 0.9477 (m-30) cc_final: 0.9235 (m-30)
REVERT: L   88 TYR cc_start: 0.9456 (m-10) cc_final: 0.9051 (m-80)
REVERT: M   38 ASN cc_start: 0.9080 (p0) cc_final: 0.8780 (p0)
REVERT: M   61 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8878 (tm-30)
REVERT: M   64 GLU cc_start: 0.9081 (tp30) cc_final: 0.8360 (mm-30)
REVERT: N   40 LYS cc_start: 0.9658 (mttt) cc_final: 0.9341 (mmtt)
REVERT: N   48 ASP cc_start: 0.8746 (p0) cc_final: 0.8529 (t0)
REVERT: N   59 MET cc_start: 0.9333 (mmm) cc_final: 0.8961 (mmm)
REVERT: N   73 GLU cc_start: 0.9397 (tp30) cc_final: 0.9105 (tp30)
REVERT: N   90 GLU cc_start: 0.9240 (mp0) cc_final: 0.8916 (mp0)
REVERT: N   92 GLN cc_start: 0.8902 (mt0) cc_final: 0.8384 (mt0)
REVERT: N  117 LYS cc_start: 0.8947 (tptt) cc_final: 0.8472 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 309
  average time/residue: 0.1478
  time to fit residues: 68.9993
Evaluate side-chains
  239 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 178 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   chunk 149 optimal weight:    6.9990
   chunk 74 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0170
   overall best weight:    0.9222

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 325 GLN
A 342 ASN
B 295 GLN
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  68 GLN
M  94 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.076942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.051760 restraints weight = 117289.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.053496 restraints weight = 63702.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.054612 restraints weight = 41786.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.055372 restraints weight = 31150.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.055815 restraints weight = 25524.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.7970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  20743  Z= 0.142
  Angle     :  0.570   8.635  29274  Z= 0.323
  Chirality :  0.039   0.245   3285
  Planarity :  0.004   0.088   2701
  Dihedral  : 27.003 175.916   5080
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.82 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.20), residues: 1717
  helix:  1.45 (0.22), residues: 562
  sheet: -1.83 (0.32), residues: 257
  loop : -2.18 (0.19), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  30 
 TYR   0.013   0.001   TYR A 265 
 PHE   0.022   0.001   PHE J  62 
 TRP   0.008   0.001   TRP A 279 
 HIS   0.018   0.001   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (20743)
  covalent geometry    : angle       0.57025 (29274)
  hydrogen bonds       : bond        0.04475 (  839)
  hydrogen bonds       : angle       3.43370 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 314
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9675 (m-40) cc_final: 0.9058 (p0)
REVERT: A  273 GLN cc_start: 0.8466 (mt0) cc_final: 0.7798 (pm20)
REVERT: A  276 LEU cc_start: 0.8498 (mm) cc_final: 0.7873 (tp)
REVERT: B  154 ARG cc_start: 0.4900 (mmt90) cc_final: 0.4646 (mmt90)
REVERT: C 3779 ASN cc_start: 0.4354 (t0) cc_final: 0.3042 (p0)
REVERT: C 3784 LYS cc_start: 0.3615 (ttmm) cc_final: 0.2843 (mttt)
REVERT: C 3818 MET cc_start: 0.8945 (mtm) cc_final: 0.8577 (mtm)
REVERT: C 3897 MET cc_start: 0.4744 (ttm) cc_final: 0.4332 (ttp)
REVERT: C 3932 ARG cc_start: 0.7937 (mpp80) cc_final: 0.7656 (ppt170)
REVERT: D  315 MET cc_start: 0.6442 (ttp) cc_final: 0.5731 (ttp)
REVERT: D  336 MET cc_start: 0.2104 (tmm) cc_final: 0.1848 (tmm)
REVERT: D  461 LYS cc_start: 0.5003 (pttm) cc_final: 0.4598 (ptmt)
REVERT: G   50 GLU cc_start: 0.9301 (tp30) cc_final: 0.8625 (tm-30)
REVERT: G   56 LYS cc_start: 0.8924 (tppp) cc_final: 0.8569 (tppp)
REVERT: G   76 GLN cc_start: 0.8896 (tt0) cc_final: 0.8165 (tp-100)
REVERT: G   92 LEU cc_start: 0.9580 (mt) cc_final: 0.9368 (mt)
REVERT: G  112 ILE cc_start: 0.9192 (mm) cc_final: 0.8976 (mm)
REVERT: G  120 MET cc_start: 0.7180 (mtt) cc_final: 0.6521 (mtt)
REVERT: H   44 LYS cc_start: 0.8874 (tppp) cc_final: 0.8435 (tppt)
REVERT: H   49 LEU cc_start: 0.9241 (mt) cc_final: 0.8962 (mt)
REVERT: H   79 LYS cc_start: 0.9225 (mttt) cc_final: 0.8643 (mtmm)
REVERT: H   88 TYR cc_start: 0.9276 (m-10) cc_final: 0.8893 (m-80)
REVERT: H   92 ARG cc_start: 0.9392 (mtp-110) cc_final: 0.9012 (ttp80)
REVERT: H   95 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8594 (mtt90)
REVERT: I   56 GLU cc_start: 0.8636 (tt0) cc_final: 0.8246 (tm-30)
REVERT: I   64 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9006 (tm-30)
REVERT: I   68 ASN cc_start: 0.9433 (t0) cc_final: 0.9216 (t0)
REVERT: I   74 LYS cc_start: 0.9079 (tttp) cc_final: 0.8512 (tptp)
REVERT: J   32 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8640 (tp30)
REVERT: J   59 MET cc_start: 0.9461 (mmp) cc_final: 0.9211 (mmm)
REVERT: J   61 SER cc_start: 0.9640 (m) cc_final: 0.9229 (p)
REVERT: J   76 ARG cc_start: 0.9439 (ttm110) cc_final: 0.9103 (ttm110)
REVERT: J   83 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8380 (tpp80)
REVERT: K   60 LEU cc_start: 0.8516 (mm) cc_final: 0.8220 (mm)
REVERT: K   61 LEU cc_start: 0.9568 (mm) cc_final: 0.9313 (mm)
REVERT: K   62 ILE cc_start: 0.8690 (mp) cc_final: 0.8350 (mp)
REVERT: K   76 GLN cc_start: 0.9196 (tt0) cc_final: 0.8883 (tp-100)
REVERT: K   94 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9117 (mt-10)
REVERT: K   97 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8018 (mp0)
REVERT: L   44 LYS cc_start: 0.9100 (mttm) cc_final: 0.8633 (mmtt)
REVERT: L   53 GLU cc_start: 0.9607 (tp30) cc_final: 0.9298 (tp30)
REVERT: L   63 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8306 (mt-10)
REVERT: L   68 ASP cc_start: 0.9436 (m-30) cc_final: 0.9023 (m-30)
REVERT: L   88 TYR cc_start: 0.9476 (m-10) cc_final: 0.8994 (m-80)
REVERT: M   61 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8784 (tm-30)
REVERT: M   64 GLU cc_start: 0.9021 (tp30) cc_final: 0.8296 (mm-30)
REVERT: N   40 LYS cc_start: 0.9650 (mttt) cc_final: 0.9341 (mmtt)
REVERT: N   48 ASP cc_start: 0.8735 (p0) cc_final: 0.8477 (t0)
REVERT: N   59 MET cc_start: 0.9295 (mmm) cc_final: 0.8917 (mmm)
REVERT: N   73 GLU cc_start: 0.9357 (tp30) cc_final: 0.9009 (tp30)
REVERT: N   90 GLU cc_start: 0.9248 (mp0) cc_final: 0.8914 (mp0)
REVERT: N   92 GLN cc_start: 0.8812 (mt0) cc_final: 0.8346 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 315
  average time/residue: 0.1417
  time to fit residues: 67.4534
Evaluate side-chains
  242 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 126 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 180 optimal weight:    4.9990
   chunk 136 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 158 optimal weight:    0.0980
   chunk 123 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 GLN
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
I  89 ASN
K  68 GLN
N  81 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.074533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.049655 restraints weight = 120853.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.051338 restraints weight = 64180.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.052472 restraints weight = 41531.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.053223 restraints weight = 30667.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.053660 restraints weight = 24862.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.8461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  20743  Z= 0.192
  Angle     :  0.606   7.968  29274  Z= 0.342
  Chirality :  0.040   0.252   3285
  Planarity :  0.004   0.085   2701
  Dihedral  : 26.954 175.719   5080
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.14 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.20), residues: 1717
  helix:  1.22 (0.22), residues: 562
  sheet: -1.81 (0.32), residues: 255
  loop : -2.14 (0.19), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C3821 
 TYR   0.012   0.001   TYR D 460 
 PHE   0.017   0.001   PHE H  61 
 TRP   0.006   0.001   TRP B 273 
 HIS   0.019   0.001   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (20743)
  covalent geometry    : angle       0.60606 (29274)
  hydrogen bonds       : bond        0.05535 (  839)
  hydrogen bonds       : angle       3.65427 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 294
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9653 (m-40) cc_final: 0.8832 (t0)
REVERT: A  273 GLN cc_start: 0.8575 (mt0) cc_final: 0.7845 (pm20)
REVERT: B  154 ARG cc_start: 0.4703 (mmt90) cc_final: 0.4423 (mmt90)
REVERT: C 3779 ASN cc_start: 0.4458 (t0) cc_final: 0.3223 (p0)
REVERT: C 3784 LYS cc_start: 0.3726 (ttmm) cc_final: 0.2794 (mttt)
REVERT: C 3812 MET cc_start: 0.7159 (ptp) cc_final: 0.6897 (ptp)
REVERT: C 3897 MET cc_start: 0.4812 (ttm) cc_final: 0.4409 (ttp)
REVERT: D  315 MET cc_start: 0.6480 (ttp) cc_final: 0.5721 (ttp)
REVERT: D  327 TRP cc_start: 0.7236 (m-10) cc_final: 0.6805 (m-10)
REVERT: D  336 MET cc_start: 0.2269 (tmm) cc_final: 0.1988 (tmm)
REVERT: G   50 GLU cc_start: 0.9289 (tp30) cc_final: 0.8633 (tm-30)
REVERT: G   56 LYS cc_start: 0.8955 (tppp) cc_final: 0.8644 (tppp)
REVERT: G   76 GLN cc_start: 0.8921 (tt0) cc_final: 0.8329 (tp-100)
REVERT: G   77 ASP cc_start: 0.9416 (p0) cc_final: 0.9213 (p0)
REVERT: G   97 GLU cc_start: 0.9017 (mp0) cc_final: 0.8716 (mp0)
REVERT: H   49 LEU cc_start: 0.9356 (mt) cc_final: 0.8873 (mt)
REVERT: H   79 LYS cc_start: 0.9264 (mttt) cc_final: 0.8694 (mtmm)
REVERT: H   84 MET cc_start: 0.8946 (mpp) cc_final: 0.8657 (mpp)
REVERT: H   88 TYR cc_start: 0.9276 (m-10) cc_final: 0.8808 (m-80)
REVERT: H   92 ARG cc_start: 0.9484 (mtp-110) cc_final: 0.8983 (ttp80)
REVERT: I   56 GLU cc_start: 0.9011 (tt0) cc_final: 0.8752 (tm-30)
REVERT: I   64 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9007 (tm-30)
REVERT: I   68 ASN cc_start: 0.9530 (t160) cc_final: 0.9285 (t0)
REVERT: I   74 LYS cc_start: 0.9093 (tttp) cc_final: 0.8583 (tptp)
REVERT: J   32 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8622 (tp30)
REVERT: J   59 MET cc_start: 0.9453 (mmp) cc_final: 0.9220 (mmm)
REVERT: J   61 SER cc_start: 0.9576 (m) cc_final: 0.9272 (p)
REVERT: J   76 ARG cc_start: 0.9435 (ttm110) cc_final: 0.9097 (ttm110)
REVERT: J   77 LEU cc_start: 0.9582 (mt) cc_final: 0.9275 (mt)
REVERT: J   83 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8416 (tpp80)
REVERT: K   50 GLU cc_start: 0.8599 (pt0) cc_final: 0.8138 (mm-30)
REVERT: K   60 LEU cc_start: 0.8479 (mm) cc_final: 0.8273 (mm)
REVERT: K   61 LEU cc_start: 0.9540 (mm) cc_final: 0.9321 (mm)
REVERT: K   62 ILE cc_start: 0.8716 (mp) cc_final: 0.8373 (mp)
REVERT: K   68 GLN cc_start: 0.9510 (pt0) cc_final: 0.9239 (pt0)
REVERT: K   76 GLN cc_start: 0.9188 (tt0) cc_final: 0.8985 (tp-100)
REVERT: K   94 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9126 (mt-10)
REVERT: K   97 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8040 (mp0)
REVERT: L   39 ARG cc_start: 0.9397 (mmt180) cc_final: 0.8868 (mmt180)
REVERT: L   44 LYS cc_start: 0.9174 (mttm) cc_final: 0.8884 (mttt)
REVERT: L   51 TYR cc_start: 0.8176 (m-80) cc_final: 0.7940 (m-10)
REVERT: L   53 GLU cc_start: 0.9652 (tp30) cc_final: 0.9388 (tp30)
REVERT: L   59 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8441 (mmmt)
REVERT: L   63 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8392 (mt-10)
REVERT: L   68 ASP cc_start: 0.9406 (m-30) cc_final: 0.8847 (m-30)
REVERT: L   88 TYR cc_start: 0.9417 (m-10) cc_final: 0.8962 (m-80)
REVERT: M   61 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8826 (tm-30)
REVERT: M   64 GLU cc_start: 0.8994 (tp30) cc_final: 0.8301 (mm-30)
REVERT: N   40 LYS cc_start: 0.9643 (mttt) cc_final: 0.9322 (mmtt)
REVERT: N   48 ASP cc_start: 0.8856 (p0) cc_final: 0.8618 (t0)
REVERT: N   59 MET cc_start: 0.9329 (mmm) cc_final: 0.8946 (mmm)
REVERT: N   73 GLU cc_start: 0.9338 (tp30) cc_final: 0.8961 (tp30)
REVERT: N   90 GLU cc_start: 0.9227 (mp0) cc_final: 0.8941 (mp0)
REVERT: N   92 GLN cc_start: 0.8863 (mt0) cc_final: 0.8622 (mt0)
  outliers start: 2
  outliers final: 0
  residues processed: 296
  average time/residue: 0.1455
  time to fit residues: 65.2958
Evaluate side-chains
  230 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 59 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 142 optimal weight:    3.9990
   chunk 110 optimal weight:    0.7980
   chunk 147 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
A 325 GLN
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
K  68 GLN
N  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.072754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.048532 restraints weight = 121811.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.050149 restraints weight = 66138.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.051184 restraints weight = 43381.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.051872 restraints weight = 32458.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.052359 restraints weight = 26721.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.9122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  20743  Z= 0.214
  Angle     :  0.640  13.811  29274  Z= 0.358
  Chirality :  0.041   0.266   3285
  Planarity :  0.005   0.087   2701
  Dihedral  : 27.121 175.849   5080
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.81 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.20), residues: 1717
  helix:  1.03 (0.21), residues: 567
  sheet: -1.73 (0.30), residues: 283
  loop : -2.10 (0.19), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C3819 
 TYR   0.027   0.002   TYR G  99 
 PHE   0.026   0.002   PHE G 104 
 TRP   0.012   0.001   TRP B 273 
 HIS   0.018   0.002   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (20743)
  covalent geometry    : angle       0.64032 (29274)
  hydrogen bonds       : bond        0.05898 (  839)
  hydrogen bonds       : angle       3.80497 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 285
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9661 (m-40) cc_final: 0.8854 (t0)
REVERT: C 3779 ASN cc_start: 0.4474 (t0) cc_final: 0.3018 (p0)
REVERT: C 3897 MET cc_start: 0.4985 (ttm) cc_final: 0.4578 (ttp)
REVERT: D  315 MET cc_start: 0.5847 (ttp) cc_final: 0.5505 (ttp)
REVERT: D  327 TRP cc_start: 0.7193 (m-10) cc_final: 0.6834 (m-10)
REVERT: D  336 MET cc_start: 0.2239 (tmm) cc_final: 0.1963 (tmm)
REVERT: G   50 GLU cc_start: 0.9288 (tp30) cc_final: 0.8598 (tm-30)
REVERT: G   56 LYS cc_start: 0.8971 (tppp) cc_final: 0.8665 (tppp)
REVERT: G   76 GLN cc_start: 0.8929 (tt0) cc_final: 0.8472 (tp-100)
REVERT: G   79 LYS cc_start: 0.8564 (tppt) cc_final: 0.8284 (tptt)
REVERT: G   89 VAL cc_start: 0.9871 (t) cc_final: 0.9618 (t)
REVERT: G   93 GLN cc_start: 0.9331 (mt0) cc_final: 0.8939 (mt0)
REVERT: G  120 MET cc_start: 0.7225 (mtt) cc_final: 0.6409 (mtt)
REVERT: H   49 LEU cc_start: 0.9430 (mt) cc_final: 0.8866 (mt)
REVERT: H   53 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9366 (mm-30)
REVERT: H   79 LYS cc_start: 0.9260 (mttt) cc_final: 0.8751 (mtmm)
REVERT: H   84 MET cc_start: 0.8972 (mpp) cc_final: 0.8747 (mpp)
REVERT: H   88 TYR cc_start: 0.9336 (m-10) cc_final: 0.8935 (m-80)
REVERT: H   92 ARG cc_start: 0.9497 (mtp-110) cc_final: 0.9011 (ttp80)
REVERT: I   64 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8989 (tm-30)
REVERT: I   68 ASN cc_start: 0.9443 (t160) cc_final: 0.9233 (t0)
REVERT: I   74 LYS cc_start: 0.9108 (tttp) cc_final: 0.8615 (tptp)
REVERT: I   90 ASP cc_start: 0.8983 (t70) cc_final: 0.8767 (t70)
REVERT: J   32 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8558 (tp30)
REVERT: J   61 SER cc_start: 0.9580 (m) cc_final: 0.9313 (p)
REVERT: J   76 ARG cc_start: 0.9436 (ttm110) cc_final: 0.9095 (ttm110)
REVERT: J   83 ARG cc_start: 0.8794 (tpp-160) cc_final: 0.8418 (tpp80)
REVERT: J  110 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8644 (tm-30)
REVERT: K   61 LEU cc_start: 0.9550 (mm) cc_final: 0.9346 (mm)
REVERT: K   62 ILE cc_start: 0.8667 (mp) cc_final: 0.8346 (mp)
REVERT: K   94 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9136 (mt-10)
REVERT: K   97 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8022 (mp0)
REVERT: K  105 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: K  112 ILE cc_start: 0.9262 (mm) cc_final: 0.8979 (mm)
REVERT: L   44 LYS cc_start: 0.9077 (mttm) cc_final: 0.8739 (mttt)
REVERT: L   63 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8406 (mt-10)
REVERT: L   68 ASP cc_start: 0.9514 (m-30) cc_final: 0.9092 (p0)
REVERT: L   88 TYR cc_start: 0.9458 (m-10) cc_final: 0.9025 (m-80)
REVERT: M   61 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8833 (tm-30)
REVERT: M   64 GLU cc_start: 0.9001 (tp30) cc_final: 0.8384 (mm-30)
REVERT: M   72 ASP cc_start: 0.9566 (t70) cc_final: 0.9363 (t0)
REVERT: N   40 LYS cc_start: 0.9640 (mttt) cc_final: 0.9360 (mmtt)
REVERT: N   48 ASP cc_start: 0.8987 (p0) cc_final: 0.8693 (t0)
REVERT: N   59 MET cc_start: 0.9361 (mmm) cc_final: 0.8986 (mmm)
REVERT: N   73 GLU cc_start: 0.9360 (tp30) cc_final: 0.9045 (tp30)
REVERT: N   90 GLU cc_start: 0.9303 (mp0) cc_final: 0.8837 (mp0)
REVERT: N   92 GLN cc_start: 0.8897 (mt0) cc_final: 0.8679 (mt0)
REVERT: N  117 LYS cc_start: 0.8930 (tptt) cc_final: 0.8472 (ttpt)
  outliers start: 2
  outliers final: 0
  residues processed: 287
  average time/residue: 0.1443
  time to fit residues: 62.7368
Evaluate side-chains
  233 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 142 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 144 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 192 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 HIS
C3769 HIS
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
K  68 GLN
N  81 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.073699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.049066 restraints weight = 119188.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.050695 restraints weight = 64542.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.051795 restraints weight = 41954.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052514 restraints weight = 31153.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.052980 restraints weight = 25503.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.9270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  20743  Z= 0.167
  Angle     :  0.598   7.905  29274  Z= 0.336
  Chirality :  0.040   0.291   3285
  Planarity :  0.004   0.086   2701
  Dihedral  : 27.093 175.655   5080
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.61 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.20), residues: 1717
  helix:  1.22 (0.22), residues: 567
  sheet: -1.66 (0.32), residues: 256
  loop : -2.09 (0.19), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C3821 
 TYR   0.028   0.001   TYR G  99 
 PHE   0.022   0.001   PHE H  61 
 TRP   0.009   0.001   TRP B 273 
 HIS   0.006   0.001   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (20743)
  covalent geometry    : angle       0.59845 (29274)
  hydrogen bonds       : bond        0.04922 (  839)
  hydrogen bonds       : angle       3.55432 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9699 (m-40) cc_final: 0.8905 (t0)
REVERT: C 3779 ASN cc_start: 0.4430 (t0) cc_final: 0.3073 (p0)
REVERT: C 3897 MET cc_start: 0.4886 (ttm) cc_final: 0.4484 (ttp)
REVERT: D  315 MET cc_start: 0.5669 (ttp) cc_final: 0.5363 (ttp)
REVERT: D  327 TRP cc_start: 0.7803 (m-10) cc_final: 0.7522 (m-10)
REVERT: D  336 MET cc_start: 0.2194 (tmm) cc_final: 0.1899 (tmm)
REVERT: G   50 GLU cc_start: 0.9275 (tp30) cc_final: 0.8471 (tm-30)
REVERT: G   56 LYS cc_start: 0.8964 (tppp) cc_final: 0.8652 (tppp)
REVERT: G   76 GLN cc_start: 0.8907 (tt0) cc_final: 0.8493 (tp-100)
REVERT: G   97 GLU cc_start: 0.9063 (mp0) cc_final: 0.8863 (mp0)
REVERT: G  106 ASP cc_start: 0.8889 (m-30) cc_final: 0.8654 (m-30)
REVERT: G  119 ILE cc_start: 0.8185 (mm) cc_final: 0.7930 (mm)
REVERT: H   49 LEU cc_start: 0.9384 (mt) cc_final: 0.8783 (mt)
REVERT: H   53 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9372 (mm-30)
REVERT: H   79 LYS cc_start: 0.9200 (mttt) cc_final: 0.8815 (mtpp)
REVERT: H   84 MET cc_start: 0.9006 (mpp) cc_final: 0.8752 (mpp)
REVERT: H   88 TYR cc_start: 0.9323 (m-10) cc_final: 0.8935 (m-80)
REVERT: H   92 ARG cc_start: 0.9482 (mtp-110) cc_final: 0.8985 (ttp80)
REVERT: H   95 ARG cc_start: 0.8945 (mmm-85) cc_final: 0.8708 (mtt90)
REVERT: I   64 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9000 (tm-30)
REVERT: I   68 ASN cc_start: 0.9419 (t160) cc_final: 0.9205 (t0)
REVERT: I   74 LYS cc_start: 0.9086 (tttp) cc_final: 0.8569 (tptp)
REVERT: J   32 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8558 (tp30)
REVERT: J   59 MET cc_start: 0.9425 (mmp) cc_final: 0.9193 (mmm)
REVERT: J   61 SER cc_start: 0.9586 (m) cc_final: 0.9278 (p)
REVERT: J   76 ARG cc_start: 0.9381 (ttm110) cc_final: 0.9034 (ttm110)
REVERT: J   77 LEU cc_start: 0.9570 (mt) cc_final: 0.9336 (mt)
REVERT: J   83 ARG cc_start: 0.8769 (tpp-160) cc_final: 0.8345 (tpp80)
REVERT: J  110 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8559 (tm-30)
REVERT: K   94 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9187 (mt-10)
REVERT: K  112 ILE cc_start: 0.9197 (mm) cc_final: 0.8903 (mm)
REVERT: L   39 ARG cc_start: 0.9368 (mmt180) cc_final: 0.8889 (mmt180)
REVERT: L   44 LYS cc_start: 0.9209 (mttm) cc_final: 0.8816 (mttt)
REVERT: L   63 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8340 (mt-10)
REVERT: L   88 TYR cc_start: 0.9480 (m-10) cc_final: 0.9060 (m-80)
REVERT: M   61 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8807 (tm-30)
REVERT: M   64 GLU cc_start: 0.8989 (tp30) cc_final: 0.8363 (mm-30)
REVERT: N   40 LYS cc_start: 0.9645 (mttt) cc_final: 0.9354 (mmtt)
REVERT: N   48 ASP cc_start: 0.8899 (p0) cc_final: 0.8660 (t0)
REVERT: N   59 MET cc_start: 0.9344 (mmm) cc_final: 0.8967 (mmm)
REVERT: N   73 GLU cc_start: 0.9363 (tp30) cc_final: 0.9016 (tp30)
REVERT: N   90 GLU cc_start: 0.9280 (mp0) cc_final: 0.8976 (mp0)
REVERT: N   92 GLN cc_start: 0.8868 (mt0) cc_final: 0.8605 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1454
  time to fit residues: 62.3573
Evaluate side-chains
  238 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    5.9990
   chunk 167 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0980
   chunk 143 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 141 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9990
   chunk 105 optimal weight:    0.2980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN
B 310 HIS
D 292 HIS
** D 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
K  68 GLN
N  81 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.074352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.049698 restraints weight = 118917.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.051362 restraints weight = 64342.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.052437 restraints weight = 42072.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.053175 restraints weight = 31250.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.053602 restraints weight = 25528.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.9479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  20743  Z= 0.155
  Angle     :  0.588   8.773  29274  Z= 0.328
  Chirality :  0.039   0.303   3285
  Planarity :  0.004   0.086   2701
  Dihedral  : 27.033 174.772   5080
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.34 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.20), residues: 1717
  helix:  1.38 (0.22), residues: 568
  sheet: -1.53 (0.32), residues: 256
  loop : -2.04 (0.19), residues: 893

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C3821 
 TYR   0.029   0.001   TYR A 265 
 PHE   0.028   0.001   PHE G 104 
 TRP   0.013   0.001   TRP B 273 
 HIS   0.005   0.001   HIS K 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (20743)
  covalent geometry    : angle       0.58787 (29274)
  hydrogen bonds       : bond        0.04531 (  839)
  hydrogen bonds       : angle       3.41706 ( 2107)

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

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

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3434 Ramachandran restraints generated.
    1717 Oldfield, 0 Emsley, 1717 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 288
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 ASN cc_start: 0.9575 (m-40) cc_final: 0.9057 (p0)
REVERT: A  273 GLN cc_start: 0.8502 (mt0) cc_final: 0.7865 (pm20)
REVERT: B  154 ARG cc_start: 0.4502 (mmp80) cc_final: 0.4124 (mmp-170)
REVERT: C 3779 ASN cc_start: 0.4627 (t0) cc_final: 0.3281 (p0)
REVERT: C 3897 MET cc_start: 0.4609 (ttm) cc_final: 0.4235 (ttp)
REVERT: D  315 MET cc_start: 0.5623 (ttp) cc_final: 0.5287 (ttp)
REVERT: D  327 TRP cc_start: 0.7690 (m-10) cc_final: 0.7368 (m-10)
REVERT: G   50 GLU cc_start: 0.9290 (tp30) cc_final: 0.8399 (tm-30)
REVERT: G   56 LYS cc_start: 0.8966 (tppp) cc_final: 0.8646 (tppp)
REVERT: G   76 GLN cc_start: 0.8952 (tt0) cc_final: 0.8472 (tp-100)
REVERT: G   89 VAL cc_start: 0.9862 (t) cc_final: 0.9635 (t)
REVERT: G   93 GLN cc_start: 0.9250 (mt0) cc_final: 0.8736 (mt0)
REVERT: H   49 LEU cc_start: 0.9350 (mt) cc_final: 0.8749 (mt)
REVERT: H   79 LYS cc_start: 0.9111 (mttt) cc_final: 0.8891 (mtpp)
REVERT: H   84 MET cc_start: 0.9027 (mpp) cc_final: 0.8757 (mpp)
REVERT: H   88 TYR cc_start: 0.9339 (m-10) cc_final: 0.8964 (m-80)
REVERT: H   92 ARG cc_start: 0.9457 (mtp-110) cc_final: 0.8948 (ttp80)
REVERT: I   64 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8975 (tm-30)
REVERT: I   68 ASN cc_start: 0.9392 (t160) cc_final: 0.9149 (t0)
REVERT: I   74 LYS cc_start: 0.9082 (tttp) cc_final: 0.8566 (tptp)
REVERT: I   90 ASP cc_start: 0.9036 (t70) cc_final: 0.8792 (t70)
REVERT: J   32 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8780 (mm-30)
REVERT: J   59 MET cc_start: 0.9434 (mmp) cc_final: 0.9200 (mmm)
REVERT: J   76 ARG cc_start: 0.9393 (ttm110) cc_final: 0.9075 (ttm110)
REVERT: J   83 ARG cc_start: 0.8721 (tpp-160) cc_final: 0.8303 (tpp80)
REVERT: J  110 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8527 (tm-30)
REVERT: K   68 GLN cc_start: 0.9556 (pt0) cc_final: 0.9254 (pt0)
REVERT: K   94 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9173 (mt-10)
REVERT: K  112 ILE cc_start: 0.9155 (mm) cc_final: 0.8867 (mm)
REVERT: K  129 ARG cc_start: 0.9338 (ttt-90) cc_final: 0.9032 (ttp80)
REVERT: L   44 LYS cc_start: 0.9227 (mttm) cc_final: 0.8694 (mttt)
REVERT: L   63 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8352 (mt-10)
REVERT: L   68 ASP cc_start: 0.9379 (m-30) cc_final: 0.9162 (m-30)
REVERT: L   88 TYR cc_start: 0.9505 (m-10) cc_final: 0.9113 (m-80)
REVERT: M   61 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8827 (tm-30)
REVERT: M   64 GLU cc_start: 0.8975 (tp30) cc_final: 0.8289 (mm-30)
REVERT: N   40 LYS cc_start: 0.9639 (mttt) cc_final: 0.9301 (mmtt)
REVERT: N   48 ASP cc_start: 0.8857 (p0) cc_final: 0.8656 (t0)
REVERT: N   59 MET cc_start: 0.9337 (mmm) cc_final: 0.8919 (mmm)
REVERT: N   73 GLU cc_start: 0.9395 (tp30) cc_final: 0.9156 (tp30)
REVERT: N   90 GLU cc_start: 0.9226 (mp0) cc_final: 0.8897 (mp0)
REVERT: N   92 GLN cc_start: 0.8860 (mt0) cc_final: 0.8549 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1476
  time to fit residues: 64.4117
Evaluate side-chains
  240 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 56 optimal weight:   30.0000
   chunk 153 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 176 optimal weight:    5.9990
   chunk 139 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 187 optimal weight:    4.9990
   chunk 94 optimal weight:   10.0000
   chunk 124 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 285 ASN
B 310 HIS
** C3822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  68 ASN
J  81 ASN
K  68 GLN
N  81 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.070249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.046169 restraints weight = 124497.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.047720 restraints weight = 67607.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.048799 restraints weight = 44180.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.049478 restraints weight = 32868.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.049917 restraints weight = 26958.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          1.0131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  20743  Z= 0.274
  Angle     :  0.700   9.759  29274  Z= 0.391
  Chirality :  0.043   0.280   3285
  Planarity :  0.005   0.083   2701
  Dihedral  : 27.445 174.966   5080
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.27 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.67 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.19), residues: 1717
  helix:  0.79 (0.21), residues: 562
  sheet: -1.44 (0.32), residues: 267
  loop : -2.18 (0.18), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C3821 
 TYR   0.029   0.002   TYR A 265 
 PHE   0.035   0.002   PHE G 104 
 TRP   0.017   0.002   TRP A  35 
 HIS   0.022   0.002   HIS C3822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (20743)
  covalent geometry    : angle       0.69989 (29274)
  hydrogen bonds       : bond        0.07074 (  839)
  hydrogen bonds       : angle       4.20596 ( 2107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3738.97 seconds
wall clock time: 65 minutes 3.96 seconds (3903.96 seconds total)