Starting phenix.real_space_refine
on Sun May  3 00:04:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mze_48754/05_2026/9mze_48754.cif"
  }
  resolution = 2.2
  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=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5908      2.51       5
     N    1617      2.21       5
     O    1726      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9307
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1898
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2606
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 3129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3129
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 14, 'TRANS': 369}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "P"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 245
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "R"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 19
          Classifications: {'water': 19}
          Link IDs: {None: 18}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.25
  Number of scatterers: 9307
  At special positions: 0
  Unit cell: (84.32, 99.96, 177.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1726      8.00
     N    1617      7.00
     C    5908      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.03

  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: 0.69
  Conformation dependent library (CDL) restraints added in 351.2 milliseconds
  

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2200

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 12 sheets defined
      43.6% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 39
      removed outlier: 3.759A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.838A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.501A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.549A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.694A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.559A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.542A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 3.599A  pdb=" N   GLN R  37 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   THR R  51 " --> pdb=" O   GLN R  47 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 169
      removed outlier: 3.557A  pdb=" N   ILE R 147 " --> pdb=" O   PHE R 143 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE R 169 " --> pdb=" O   ILE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 173
    Processing helix  chain 'R' and resid 174 through 204
      removed outlier: 3.656A  pdb=" N   ALA R 199 " --> pdb=" O   PHE R 195 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS R 202 " --> pdb=" O   ASP R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 222
      removed outlier: 3.765A  pdb=" N   ASP R 222 " --> pdb=" O   LEU R 218 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 3.641A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL R 229 " --> pdb=" O   SER R 225 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   PHE R 230 " --> pdb=" O   CYS R 226 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN R 234 " --> pdb=" O   PHE R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 275
      removed outlier: 3.721A  pdb=" N   ARG R 267 " --> pdb=" O   GLN R 263 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL R 270 " --> pdb=" O   PHE R 266 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 292
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 294 through 298
    Processing helix  chain 'R' and resid 302 through 338
      removed outlier: 4.343A  pdb=" N   ILE R 308 " --> pdb=" O   ASN R 304 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ILE R 309 " --> pdb=" O   TYR R 305 " (cutoff:3.500A)
      Proline residue:  R 312  - end of helix
      removed outlier: 3.555A  pdb=" N   ASN R 320 " --> pdb=" O   ALA R 316 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 344 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 365
    Processing helix  chain 'R' and resid 377 through 393
      removed outlier: 3.634A  pdb=" N   PHE R 381 " --> pdb=" O   GLY R 377 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 403
    Processing helix  chain 'R' and resid 406 through 419
      removed outlier: 3.589A  pdb=" N   GLN R 410 " --> pdb=" O   ASN R 406 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.517A  pdb=" N   SER P  16 " --> pdb=" O   LYS P  12 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.602A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.572A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.466A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.724A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.925A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.752A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.825A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.607A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.892A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.637A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.918A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP N  50 " --> pdb=" O   SER N  59 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66
    Processing sheet with id=AB3, first strand: chain 'R' and resid 80 through 84

    453 hydrogen bonds defined for protein.
    1290 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1515
        1.32 -     1.45: 2743
        1.45 -     1.58: 5165
        1.58 -     1.71: 0
        1.71 -     1.84: 76
  Bond restraints: 9499
  Sorted by residual:
  bond pdb=" C   GLN R 213 "
       pdb=" N   TRP R 214 "
    ideal  model  delta    sigma   weight residual
    1.335  1.400 -0.065 1.31e-02 5.83e+03 2.44e+01
  bond pdb=" C   VAL R 319 "
       pdb=" N   ASN R 320 "
    ideal  model  delta    sigma   weight residual
    1.335  1.271  0.064 1.38e-02 5.25e+03 2.17e+01
  bond pdb=" C   PRO R 137 "
       pdb=" O   PRO R 137 "
    ideal  model  delta    sigma   weight residual
    1.235  1.190  0.045 1.11e-02 8.12e+03 1.65e+01
  bond pdb=" N   ARG R 102 "
       pdb=" CA  ARG R 102 "
    ideal  model  delta    sigma   weight residual
    1.455  1.504 -0.049 1.29e-02 6.01e+03 1.47e+01
  bond pdb=" C   LYS R 346 "
       pdb=" N   CYS R 347 "
    ideal  model  delta    sigma   weight residual
    1.335  1.287  0.048 1.36e-02 5.41e+03 1.23e+01
  ... (remaining 9494 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 12280
        1.88 -     3.77: 507
        3.77 -     5.65: 69
        5.65 -     7.54: 18
        7.54 -     9.42: 3
  Bond angle restraints: 12877
  Sorted by residual:
  angle pdb=" N   GLU A  50 "
        pdb=" CA  GLU A  50 "
        pdb=" C   GLU A  50 "
      ideal   model   delta    sigma   weight residual
     112.92  103.50    9.42 1.23e+00 6.61e-01 5.87e+01
  angle pdb=" N   PRO R 137 "
        pdb=" CA  PRO R 137 "
        pdb=" C   PRO R 137 "
      ideal   model   delta    sigma   weight residual
     114.92  107.48    7.44 1.19e+00 7.06e-01 3.91e+01
  angle pdb=" N   SER R 301 "
        pdb=" CA  SER R 301 "
        pdb=" C   SER R 301 "
      ideal   model   delta    sigma   weight residual
     111.14  117.53   -6.39 1.08e+00 8.57e-01 3.50e+01
  angle pdb=" N   CYS R  62 "
        pdb=" CA  CYS R  62 "
        pdb=" C   CYS R  62 "
      ideal   model   delta    sigma   weight residual
     109.96  101.72    8.24 1.50e+00 4.44e-01 3.02e+01
  angle pdb=" CA  PHE R 195 "
        pdb=" CB  PHE R 195 "
        pdb=" CG  PHE R 195 "
      ideal   model   delta    sigma   weight residual
     113.80  118.65   -4.85 1.00e+00 1.00e+00 2.35e+01
  ... (remaining 12872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.63: 5091
       16.63 -    33.25: 416
       33.25 -    49.88: 80
       49.88 -    66.50: 22
       66.50 -    83.13: 9
  Dihedral angle restraints: 5618
    sinusoidal: 2218
      harmonic: 3400
  Sorted by residual:
  dihedral pdb=" CA  LEU B 117 "
           pdb=" C   LEU B 117 "
           pdb=" N   ASP B 118 "
           pdb=" CA  ASP B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.81   22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.49   21.51     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" C   TYR R 148 "
           pdb=" N   TYR R 148 "
           pdb=" CA  TYR R 148 "
           pdb=" CB  TYR R 148 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.11   10.51     0      2.50e+00 1.60e-01 1.77e+01
  ... (remaining 5615 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1156
       0.062 -    0.123: 207
       0.123 -    0.185: 39
       0.185 -    0.247: 10
       0.247 -    0.308: 6
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  SER R 301 "
            pdb=" N   SER R 301 "
            pdb=" C   SER R 301 "
            pdb=" CB  SER R 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CA  TYR R 148 "
            pdb=" N   TYR R 148 "
            pdb=" C   TYR R 148 "
            pdb=" CB  TYR R 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  TYR A 253 "
            pdb=" N   TYR A 253 "
            pdb=" C   TYR A 253 "
            pdb=" CB  TYR A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1415 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET P  27 "    0.019 2.00e-02 2.50e+03   3.77e-02 1.42e+01
        pdb=" C   MET P  27 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   MET P  27 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ASN P  28 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 305 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.04e+00
        pdb=" C   TYR R 305 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   TYR R 305 "    0.019 2.00e-02 2.50e+03
        pdb=" N   TRP R 306 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 318 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.52e+00
        pdb=" C   GLY R 318 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLY R 318 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL R 319 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2376
        2.81 -     3.33: 8234
        3.33 -     3.85: 14489
        3.85 -     4.38: 18183
        4.38 -     4.90: 29770
  Nonbonded interactions: 73052
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 183 "
            pdb=" OG1 THR B 184 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" N   LYS A 293 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" O   VAL R 370 "
            pdb=" NZ  LYS R 383 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" OD1 ASP A 354 "
            pdb=" N   GLY A 355 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OE1 GLU A 344 "
            pdb=" NH1 ARG A 347 "
     model   vdw
     2.376 3.120
  ... (remaining 73047 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.560
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:7.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
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   0.065   9505  Z= 0.373
  Angle     :  0.864   9.422  12889  Z= 0.568
  Chirality :  0.055   0.308   1418
  Planarity :  0.006   0.092   1640
  Dihedral  : 13.405  83.130   3400
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.11 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.22), residues: 1143
  helix: -0.58 (0.21), residues: 456
  sheet:  0.68 (0.33), residues: 214
  loop : -0.63 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 389 
 TYR   0.019   0.002   TYR A 358 
 PHE   0.025   0.002   PHE R 195 
 TRP   0.022   0.002   TRP B 339 
 HIS   0.015   0.002   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 9499)
  covalent geometry    : angle       0.86384 (12877)
  SS BOND              : bond        0.00547 (    6)
  SS BOND              : angle       1.39936 (   12)
  hydrogen bonds       : bond        0.30121 (  453)
  hydrogen bonds       : angle       7.16588 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 0.277 
Fit side-chains
REVERT: R  347 CYS cc_start: 0.7238 (t) cc_final: 0.6793 (p)
REVERT: R  414 ARG cc_start: 0.6237 (mtt-85) cc_final: 0.5857 (mtt-85)
  outliers start: 2
  outliers final: 0
  residues processed: 123
  average time/residue: 0.8197
  time to fit residues: 105.7426
Evaluate side-chains
  104 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
G  18 GLN
R 173 HIS
P  28 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.221652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.154716 restraints weight = 8285.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.69
r_work: 0.3686 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3579 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9505  Z= 0.154
  Angle     :  0.577   6.778  12889  Z= 0.324
  Chirality :  0.043   0.151   1418
  Planarity :  0.004   0.046   1640
  Dihedral  :  4.642  21.614   1276
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.04 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.23), residues: 1143
  helix:  1.65 (0.23), residues: 462
  sheet:  1.15 (0.34), residues: 213
  loop : -0.55 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 310 
 TYR   0.022   0.001   TYR R 148 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.018   0.002   TRP A 234 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9499)
  covalent geometry    : angle       0.57692 (12877)
  SS BOND              : bond        0.00297 (    6)
  SS BOND              : angle       0.98612 (   12)
  hydrogen bonds       : bond        0.07802 (  453)
  hydrogen bonds       : angle       4.59287 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 0.350 
Fit side-chains
REVERT: R  414 ARG cc_start: 0.5911 (mtt-85) cc_final: 0.5551 (mtt-85)
  outliers start: 7
  outliers final: 2
  residues processed: 121
  average time/residue: 0.8207
  time to fit residues: 104.1569
Evaluate side-chains
  112 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  287 VAL
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 91 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0270
   chunk 51 optimal weight:    0.0980
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 105 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 75 optimal weight:   30.0000
   chunk 16 optimal weight:    9.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.4438

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 220 HIS
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
R 140 GLN
R 410 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.225088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.160783 restraints weight = 8403.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 1.87
r_work: 0.3731 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3630 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9505  Z= 0.116
  Angle     :  0.472   5.831  12889  Z= 0.264
  Chirality :  0.040   0.137   1418
  Planarity :  0.003   0.044   1640
  Dihedral  :  4.149  19.391   1276
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.55 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.24), residues: 1143
  helix:  2.43 (0.24), residues: 464
  sheet:  1.21 (0.34), residues: 213
  loop : -0.48 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 310 
 TYR   0.018   0.001   TYR R 148 
 PHE   0.013   0.001   PHE R 315 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9499)
  covalent geometry    : angle       0.47192 (12877)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       0.84467 (   12)
  hydrogen bonds       : bond        0.05701 (  453)
  hydrogen bonds       : angle       4.00629 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7695 (t0)
REVERT: A  392 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7403 (mm-30)
REVERT: B  217 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6617 (pmt)
REVERT: N    3 GLN cc_start: 0.6903 (mt0) cc_final: 0.6513 (mm-40)
REVERT: R  414 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5468 (mtt-85)
  outliers start: 9
  outliers final: 2
  residues processed: 123
  average time/residue: 0.8315
  time to fit residues: 107.0990
Evaluate side-chains
  110 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 77 optimal weight:    8.9990
   chunk 87 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0030
   chunk 97 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 102 optimal weight:    0.3980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
R 410 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.224731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.160150 restraints weight = 8500.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 2.10
r_work: 0.3717 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3616 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9505  Z= 0.113
  Angle     :  0.478   6.465  12889  Z= 0.265
  Chirality :  0.040   0.144   1418
  Planarity :  0.003   0.045   1640
  Dihedral  :  4.094  19.126   1276
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 10.05 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.24), residues: 1143
  helix:  2.68 (0.24), residues: 464
  sheet:  1.25 (0.33), residues: 214
  loop : -0.42 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 389 
 TYR   0.027   0.001   TYR R 148 
 PHE   0.020   0.001   PHE R 385 
 TRP   0.014   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9499)
  covalent geometry    : angle       0.47718 (12877)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       0.82293 (   12)
  hydrogen bonds       : bond        0.05295 (  453)
  hydrogen bonds       : angle       3.90635 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7618 (t0)
REVERT: A  392 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7412 (mm-30)
REVERT: B  217 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6616 (pmt)
REVERT: G   17 GLU cc_start: 0.6957 (tt0) cc_final: 0.6536 (mm-30)
REVERT: G   21 MET cc_start: 0.6891 (mtp) cc_final: 0.6191 (mtm)
REVERT: N    3 GLN cc_start: 0.6937 (mt0) cc_final: 0.6541 (mm-40)
REVERT: R  410 GLN cc_start: 0.7326 (mt0) cc_final: 0.7122 (mt0)
REVERT: R  414 ARG cc_start: 0.5940 (mtt-85) cc_final: 0.5397 (mtt-85)
  outliers start: 11
  outliers final: 4
  residues processed: 116
  average time/residue: 0.8443
  time to fit residues: 102.6341
Evaluate side-chains
  111 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:   20.0000
   chunk 66 optimal weight:    0.2980
   chunk 79 optimal weight:    8.9990
   chunk 47 optimal weight:    8.9990
   chunk 9 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
B 125 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.219765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.153948 restraints weight = 8328.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.03
r_work: 0.3640 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3538 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9505  Z= 0.160
  Angle     :  0.577   6.630  12889  Z= 0.321
  Chirality :  0.044   0.160   1418
  Planarity :  0.004   0.048   1640
  Dihedral  :  4.505  21.913   1276
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.16 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.24), residues: 1143
  helix:  2.61 (0.24), residues: 457
  sheet:  1.04 (0.34), residues: 209
  loop : -0.33 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 265 
 TYR   0.026   0.002   TYR R 148 
 PHE   0.019   0.002   PHE B 151 
 TRP   0.019   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9499)
  covalent geometry    : angle       0.57661 (12877)
  SS BOND              : bond        0.00454 (    6)
  SS BOND              : angle       1.03976 (   12)
  hydrogen bonds       : bond        0.06798 (  453)
  hydrogen bonds       : angle       4.20416 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7810 (t0)
REVERT: B  217 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6795 (pmt)
REVERT: G   17 GLU cc_start: 0.6951 (tt0) cc_final: 0.6642 (mm-30)
REVERT: N    3 GLN cc_start: 0.6901 (mt0) cc_final: 0.6519 (mm-40)
REVERT: R  410 GLN cc_start: 0.7337 (mt0) cc_final: 0.7018 (mt0)
REVERT: R  414 ARG cc_start: 0.5964 (mtt-85) cc_final: 0.5294 (mtt-85)
REVERT: P   27 MET cc_start: 0.2878 (tpt) cc_final: 0.2662 (ttt)
  outliers start: 12
  outliers final: 6
  residues processed: 111
  average time/residue: 0.8636
  time to fit residues: 100.7025
Evaluate side-chains
  105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0050
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 ASN
A 390 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.221760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.156448 restraints weight = 8410.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.06
r_work: 0.3669 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9505  Z= 0.129
  Angle     :  0.506   6.545  12889  Z= 0.283
  Chirality :  0.041   0.151   1418
  Planarity :  0.004   0.047   1640
  Dihedral  :  4.305  20.653   1276
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.16 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.24), residues: 1143
  helix:  2.71 (0.24), residues: 458
  sheet:  1.24 (0.34), residues: 201
  loop : -0.36 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.026   0.001   TYR R 148 
 PHE   0.015   0.001   PHE R 385 
 TRP   0.019   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9499)
  covalent geometry    : angle       0.50580 (12877)
  SS BOND              : bond        0.00347 (    6)
  SS BOND              : angle       0.91369 (   12)
  hydrogen bonds       : bond        0.05887 (  453)
  hydrogen bonds       : angle       4.00483 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7709 (t0)
REVERT: A  392 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7486 (mm-30)
REVERT: B  217 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6724 (pmt)
REVERT: G   17 GLU cc_start: 0.6839 (tt0) cc_final: 0.6584 (mm-30)
REVERT: N    3 GLN cc_start: 0.6894 (mt0) cc_final: 0.6515 (mm-40)
REVERT: R  410 GLN cc_start: 0.7318 (mt0) cc_final: 0.6985 (mt0)
REVERT: R  414 ARG cc_start: 0.5944 (mtt-85) cc_final: 0.5411 (mtt-85)
  outliers start: 13
  outliers final: 6
  residues processed: 116
  average time/residue: 0.8451
  time to fit residues: 102.9726
Evaluate side-chains
  107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 56 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 82 optimal weight:    0.0970
   overall best weight:    3.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN
P  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.215675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150040 restraints weight = 8205.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.03
r_work: 0.3577 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   9505  Z= 0.265
  Angle     :  0.763   8.232  12889  Z= 0.426
  Chirality :  0.052   0.202   1418
  Planarity :  0.006   0.069   1640
  Dihedral  :  5.059  25.021   1276
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.16 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.24), residues: 1143
  helix:  2.09 (0.23), residues: 456
  sheet:  0.83 (0.34), residues: 200
  loop : -0.53 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 374 
 TYR   0.037   0.003   TYR R 148 
 PHE   0.030   0.003   PHE B 151 
 TRP   0.025   0.003   TRP A 234 
 HIS   0.008   0.002   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 9499)
  covalent geometry    : angle       0.76233 (12877)
  SS BOND              : bond        0.00767 (    6)
  SS BOND              : angle       1.44983 (   12)
  hydrogen bonds       : bond        0.09061 (  453)
  hydrogen bonds       : angle       4.61623 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.7600 (mp-120) cc_final: 0.7390 (mm110)
REVERT: A  292 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8046 (t0)
REVERT: B  217 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6946 (pmt)
REVERT: N    3 GLN cc_start: 0.6888 (mt0) cc_final: 0.6485 (mm-40)
REVERT: R  410 GLN cc_start: 0.7447 (mt0) cc_final: 0.7150 (mt0)
REVERT: R  414 ARG cc_start: 0.6004 (mtt-85) cc_final: 0.5476 (mtt-85)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.8336
  time to fit residues: 96.2582
Evaluate side-chains
  105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  287 VAL
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 390 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.217299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152554 restraints weight = 8157.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.00
r_work: 0.3604 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9505  Z= 0.198
  Angle     :  0.656   7.913  12889  Z= 0.365
  Chirality :  0.046   0.170   1418
  Planarity :  0.005   0.052   1640
  Dihedral  :  4.894  23.963   1276
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.36 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.24), residues: 1143
  helix:  2.19 (0.24), residues: 456
  sheet:  0.79 (0.33), residues: 210
  loop : -0.49 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 374 
 TYR   0.029   0.002   TYR R 148 
 PHE   0.026   0.002   PHE B 151 
 TRP   0.024   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9499)
  covalent geometry    : angle       0.65486 (12877)
  SS BOND              : bond        0.00588 (    6)
  SS BOND              : angle       1.19035 (   12)
  hydrogen bonds       : bond        0.07898 (  453)
  hydrogen bonds       : angle       4.42945 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7987 (t0)
REVERT: A  392 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7703 (mm-30)
REVERT: B  217 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6978 (pmt)
REVERT: G   17 GLU cc_start: 0.6995 (tt0) cc_final: 0.6753 (mm-30)
REVERT: N    3 GLN cc_start: 0.6900 (mt0) cc_final: 0.6486 (mm-40)
REVERT: R  410 GLN cc_start: 0.7439 (mt0) cc_final: 0.7137 (mt0)
REVERT: R  414 ARG cc_start: 0.6022 (mtt-85) cc_final: 0.5491 (mtt-85)
  outliers start: 12
  outliers final: 7
  residues processed: 104
  average time/residue: 0.8613
  time to fit residues: 93.8201
Evaluate side-chains
  104 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:   50.0000
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS
P  28 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.219362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.154085 restraints weight = 8289.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.99
r_work: 0.3625 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9505  Z= 0.155
  Angle     :  0.566   6.925  12889  Z= 0.316
  Chirality :  0.043   0.158   1418
  Planarity :  0.004   0.051   1640
  Dihedral  :  4.620  22.093   1276
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.56 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.24), residues: 1143
  helix:  2.44 (0.24), residues: 457
  sheet:  0.89 (0.33), residues: 210
  loop : -0.39 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.025   0.002   TYR R 148 
 PHE   0.020   0.002   PHE B 151 
 TRP   0.022   0.002   TRP A 234 
 HIS   0.004   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9499)
  covalent geometry    : angle       0.56494 (12877)
  SS BOND              : bond        0.00441 (    6)
  SS BOND              : angle       1.04190 (   12)
  hydrogen bonds       : bond        0.06768 (  453)
  hydrogen bonds       : angle       4.21230 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7901 (t0)
REVERT: A  392 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7653 (mm-30)
REVERT: B  217 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6857 (pmt)
REVERT: G   17 GLU cc_start: 0.6912 (tt0) cc_final: 0.6694 (mm-30)
REVERT: N    3 GLN cc_start: 0.6913 (mt0) cc_final: 0.6512 (mm-40)
REVERT: R  397 MET cc_start: 0.7630 (mtm) cc_final: 0.7004 (mpt)
REVERT: R  410 GLN cc_start: 0.7397 (mt0) cc_final: 0.7107 (mt0)
REVERT: R  414 ARG cc_start: 0.6017 (mtt-85) cc_final: 0.5513 (mtt-85)
  outliers start: 11
  outliers final: 7
  residues processed: 105
  average time/residue: 0.8499
  time to fit residues: 93.5611
Evaluate side-chains
  105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 85 optimal weight:    5.9990
   chunk 80 optimal weight:   30.0000
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 HIS
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.220586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156759 restraints weight = 8330.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.03
r_work: 0.3637 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9505  Z= 0.139
  Angle     :  0.540   7.912  12889  Z= 0.299
  Chirality :  0.042   0.153   1418
  Planarity :  0.004   0.050   1640
  Dihedral  :  4.450  21.525   1276
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 12.46 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.24), residues: 1143
  helix:  2.53 (0.24), residues: 458
  sheet:  1.11 (0.34), residues: 207
  loop : -0.40 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 389 
 TYR   0.025   0.001   TYR R 148 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.021   0.002   TRP A 234 
 HIS   0.003   0.001   HIS A 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9499)
  covalent geometry    : angle       0.53903 (12877)
  SS BOND              : bond        0.00383 (    6)
  SS BOND              : angle       0.93851 (   12)
  hydrogen bonds       : bond        0.06166 (  453)
  hydrogen bonds       : angle       4.08019 ( 1290)

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

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

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2286 Ramachandran restraints generated.
    1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  292 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7846 (t0)
REVERT: A  392 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7600 (mm-30)
REVERT: G   17 GLU cc_start: 0.6774 (tt0) cc_final: 0.6567 (mm-30)
REVERT: N    3 GLN cc_start: 0.6941 (mt0) cc_final: 0.6552 (mm-40)
REVERT: R  397 MET cc_start: 0.7588 (mtm) cc_final: 0.6947 (mpt)
REVERT: R  410 GLN cc_start: 0.7393 (mt0) cc_final: 0.7087 (mt0)
REVERT: R  414 ARG cc_start: 0.6005 (mtt-85) cc_final: 0.5498 (mtt-85)
  outliers start: 10
  outliers final: 7
  residues processed: 105
  average time/residue: 0.8667
  time to fit residues: 95.3645
Evaluate side-chains
  105 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain N residue  124 VAL
Chi-restraints excluded: chain R residue  148 TYR
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  362 THR
Chi-restraints excluded: chain R residue  409 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 98 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.218569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.154220 restraints weight = 8204.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 1.98
r_work: 0.3613 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9505  Z= 0.170
  Angle     :  0.600   7.054  12889  Z= 0.334
  Chirality :  0.044   0.173   1418
  Planarity :  0.004   0.052   1640
  Dihedral  :  4.667  22.935   1276
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 12.86 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.24), residues: 1143
  helix:  2.43 (0.24), residues: 458
  sheet:  0.89 (0.33), residues: 210
  loop : -0.39 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 389 
 TYR   0.028   0.002   TYR R 148 
 PHE   0.022   0.002   PHE B 151 
 TRP   0.022   0.002   TRP A 234 
 HIS   0.005   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9499)
  covalent geometry    : angle       0.59934 (12877)
  SS BOND              : bond        0.00507 (    6)
  SS BOND              : angle       1.08748 (   12)
  hydrogen bonds       : bond        0.07028 (  453)
  hydrogen bonds       : angle       4.23989 ( 1290)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6226.47 seconds
wall clock time: 106 minutes 9.48 seconds (6369.48 seconds total)