Starting phenix.real_space_refine
on Tue Mar  3 23:04:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lmk_0917/03_2026/6lmk_0917.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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      58      5.16       5
     C    5863      2.51       5
     N    1631      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 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: 9240
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1889
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1889
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2584
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 420
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "N"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 964
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 3138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3138
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 379}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 51
    Chain: "E"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 245
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
  Time building chain proxies: 1.97, per 1000 atoms: 0.21
  Number of scatterers: 9240
  At special positions: 0
  Unit cell: (97.58, 163.18, 86.92, 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      58     16.00
     O    1688      8.00
     N    1631      7.00
     C    5863      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=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  43 " - pdb=" SG  CYS R  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " 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: 0.62
  Conformation dependent library (CDL) restraints added in 314.1 milliseconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.9% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 4.404A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 3.986A  pdb=" N   THR A  55 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A  56 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 56'
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.789A  pdb=" N   ALA A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 298
      removed outlier: 3.907A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.634A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.729A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.659A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 5 through 25
      removed outlier: 4.253A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.547A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 4.455A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLN C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'N' and resid 61 through 65
      removed outlier: 3.608A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.050A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 48
    Processing helix  chain 'R' and resid 87 through 91
    Processing helix  chain 'R' and resid 117 through 122
      removed outlier: 4.487A  pdb=" N   GLN R 120 " --> pdb=" O   ASP R 117 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS R 121 " --> pdb=" O   ALA R 118 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 164
      removed outlier: 3.882A  pdb=" N   LEU R 151 " --> pdb=" O   VAL R 147 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU R 158 " --> pdb=" O   GLY R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 202
      removed outlier: 3.588A  pdb=" N   HIS R 177 " --> pdb=" O   ARG R 173 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER R 183 " --> pdb=" O   ASN R 179 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER R 190 " --> pdb=" O   LEU R 186 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   VAL R 193 " --> pdb=" O   SER R 189 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR R 202 " --> pdb=" O   LEU R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 217
    Processing helix  chain 'R' and resid 220 through 251
      removed outlier: 3.759A  pdb=" N   CYS R 224 " --> pdb=" O   ALA R 220 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL R 236 " --> pdb=" O   GLN R 232 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   TYR R 239 " --> pdb=" O   ILE R 235 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU R 249 " --> pdb=" O   GLU R 245 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 273
    Processing helix  chain 'R' and resid 273 through 289
      Proline residue:  R 281  - end of helix
    Processing helix  chain 'R' and resid 304 through 333
      Proline residue:  R 310  - end of helix
      removed outlier: 4.879A  pdb=" N   ASN R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   ILE R 321 " --> pdb=" O   ILE R 317 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL R 326 " --> pdb=" O   PHE R 322 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU R 328 " --> pdb=" O   ARG R 324 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   ALA R 331 " --> pdb=" O   GLN R 327 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 342 through 347
    Processing helix  chain 'R' and resid 374 through 402
      removed outlier: 3.535A  pdb=" N   ARG R 378 " --> pdb=" O   GLN R 374 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 419
      removed outlier: 3.565A  pdb=" N   ARG R 414 " --> pdb=" O   GLU R 410 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 13
      removed outlier: 3.853A  pdb=" N   THR E   7 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER E   8 " --> pdb=" O   GLY E   4 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 29
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 4.031A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.577A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.943A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ILE B  93 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.503A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.854A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.773A  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: 3.571A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 4.070A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.585A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.667A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 80
      removed outlier: 3.539A  pdb=" N   THR R  75 " --> pdb=" O   CYS R 100 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS R  98 " --> pdb=" O   ALA R  77 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1197 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: 1.49

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2936
        1.34 -     1.46: 2091
        1.46 -     1.58: 4340
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9447
  Sorted by residual:
  bond pdb=" CG1 ILE R 321 "
       pdb=" CD1 ILE R 321 "
    ideal  model  delta    sigma   weight residual
    1.513  1.399  0.114 3.90e-02 6.57e+02 8.58e+00
  bond pdb=" CB  TRP R 241 "
       pdb=" CG  TRP R 241 "
    ideal  model  delta    sigma   weight residual
    1.498  1.429  0.069 3.10e-02 1.04e+03 4.94e+00
  bond pdb=" CB  ILE R 355 "
       pdb=" CG2 ILE R 355 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.43e+00
  bond pdb=" CB  ASN A 239 "
       pdb=" CG  ASN A 239 "
    ideal  model  delta    sigma   weight residual
    1.516  1.464  0.052 2.50e-02 1.60e+03 4.34e+00
  bond pdb=" CB  VAL B 315 "
       pdb=" CG2 VAL B 315 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.73e+00
  ... (remaining 9442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 12135
        1.92 -     3.85: 581
        3.85 -     5.77: 59
        5.77 -     7.69: 25
        7.69 -     9.62: 10
  Bond angle restraints: 12810
  Sorted by residual:
  angle pdb=" CA  TYR R 145 "
        pdb=" CB  TYR R 145 "
        pdb=" CG  TYR R 145 "
      ideal   model   delta    sigma   weight residual
     113.90  120.39   -6.49 1.80e+00 3.09e-01 1.30e+01
  angle pdb=" C   GLN R  42 "
        pdb=" N   CYS R  43 "
        pdb=" CA  CYS R  43 "
      ideal   model   delta    sigma   weight residual
     122.06  115.58    6.48 1.86e+00 2.89e-01 1.21e+01
  angle pdb=" N   VAL R 280 "
        pdb=" CA  VAL R 280 "
        pdb=" C   VAL R 280 "
      ideal   model   delta    sigma   weight residual
     108.88  116.30   -7.42 2.16e+00 2.14e-01 1.18e+01
  angle pdb=" N   GLY R 302 "
        pdb=" CA  GLY R 302 "
        pdb=" C   GLY R 302 "
      ideal   model   delta    sigma   weight residual
     111.15  105.43    5.72 1.76e+00 3.23e-01 1.06e+01
  angle pdb=" CA  ILE R 355 "
        pdb=" C   ILE R 355 "
        pdb=" N   PRO R 356 "
      ideal   model   delta    sigma   weight residual
     118.88  123.73   -4.85 1.54e+00 4.22e-01 9.93e+00
  ... (remaining 12805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4945
       17.94 -    35.88: 523
       35.88 -    53.82: 105
       53.82 -    71.76: 12
       71.76 -    89.70: 7
  Dihedral angle restraints: 5592
    sinusoidal: 2176
      harmonic: 3416
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    5.98   87.02     1      1.00e+01 1.00e-02 9.10e+01
  dihedral pdb=" CA  CYS R  58 "
           pdb=" C   CYS R  58 "
           pdb=" N   ASN R  59 "
           pdb=" CA  ASN R  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -141.89  -38.11     0      5.00e+00 4.00e-02 5.81e+01
  dihedral pdb=" CA  PHE R 303 "
           pdb=" C   PHE R 303 "
           pdb=" N   TRP R 304 "
           pdb=" CA  TRP R 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.15   37.85     0      5.00e+00 4.00e-02 5.73e+01
  ... (remaining 5589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 977
       0.055 -    0.109: 350
       0.109 -    0.164: 75
       0.164 -    0.218: 15
       0.218 -    0.273: 2
  Chirality restraints: 1419
  Sorted by residual:
  chirality pdb=" CB  VAL A 241 "
            pdb=" CA  VAL A 241 "
            pdb=" CG1 VAL A 241 "
            pdb=" CG2 VAL A 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  ILE N  70 "
            pdb=" CA  ILE N  70 "
            pdb=" CG1 ILE N  70 "
            pdb=" CG2 ILE N  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CB  VAL R 280 "
            pdb=" CA  VAL R 280 "
            pdb=" CG1 VAL R 280 "
            pdb=" CG2 VAL R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1416 not shown)

  Planarity restraints: 1641
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 355 "   -0.049 5.00e-02 4.00e+02   7.38e-02 8.72e+00
        pdb=" N   PRO R 356 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO R 356 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R 356 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.047 5.00e-02 4.00e+02   7.08e-02 8.02e+00
        pdb=" N   PRO B 236 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R  63 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   ASP R  63 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASP R  63 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS R  64 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1638 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2835
        2.81 -     3.33: 8440
        3.33 -     3.85: 15588
        3.85 -     4.38: 17632
        4.38 -     4.90: 30462
  Nonbonded interactions: 74957
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 145 "
            pdb=" OD2 ASP R 195 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OG  SER A 251 "
            pdb=" O   LYS A 293 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   SER R 189 "
            pdb=" OG  SER R 189 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" OD1 ASP B 290 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" NE1 TRP N  47 "
            pdb=" O   SER N  49 "
     model   vdw
     2.320 3.120
  ... (remaining 74952 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.650
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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      :  0.009   0.114   9453  Z= 0.374
  Angle     :  0.962   9.616  12822  Z= 0.522
  Chirality :  0.058   0.273   1419
  Planarity :  0.007   0.074   1641
  Dihedral  : 15.097  89.701   3366
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 10.36 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.19 (0.20), residues: 1162
  helix: -2.62 (0.18), residues: 420
  sheet: -2.88 (0.31), residues: 189
  loop : -2.80 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 228 
 TYR   0.036   0.003   TYR B  59 
 PHE   0.032   0.003   PHE N 108 
 TRP   0.022   0.003   TRP R 241 
 HIS   0.013   0.002   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00868 ( 9447)
  covalent geometry    : angle       0.96034 (12810)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       1.86558 (   12)
  hydrogen bonds       : bond        0.19266 (  413)
  hydrogen bonds       : angle       8.22866 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 201
  time to evaluate  : 0.348 
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   32 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8283 (mtmm)
REVERT: A  265 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7003 (ttm110)
REVERT: A  344 GLU cc_start: 0.8015 (tp30) cc_final: 0.7789 (tp30)
REVERT: B  169 TRP cc_start: 0.8671 (m100) cc_final: 0.8399 (m100)
REVERT: B  270 ILE cc_start: 0.8485 (tp) cc_final: 0.8279 (tp)
REVERT: B  291 ASP cc_start: 0.8426 (p0) cc_final: 0.8205 (p0)
REVERT: C   17 GLU cc_start: 0.7923 (tp30) cc_final: 0.7520 (tp30)
REVERT: N   38 ARG cc_start: 0.8542 (ptt180) cc_final: 0.7914 (ptt90)
REVERT: N   76 LYS cc_start: 0.9093 (tppp) cc_final: 0.8581 (mmtp)
REVERT: N   77 ASN cc_start: 0.8547 (m110) cc_final: 0.8104 (p0)
REVERT: N   91 THR cc_start: 0.8621 (p) cc_final: 0.8364 (p)
REVERT: R  123 MET cc_start: 0.7720 (mmm) cc_final: 0.7369 (mmm)
REVERT: R  127 GLU cc_start: 0.8645 (mp0) cc_final: 0.8195 (mp0)
REVERT: R  133 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8071 (tp30)
REVERT: R  270 ILE cc_start: 0.9062 (tt) cc_final: 0.8838 (tt)
REVERT: R  410 GLU cc_start: 0.7758 (tp30) cc_final: 0.7441 (tp30)
REVERT: E   15 ASP cc_start: 0.8414 (p0) cc_final: 0.7988 (p0)
REVERT: E   17 ARG cc_start: 0.8664 (tpt90) cc_final: 0.7984 (tpp80)
REVERT: E   21 ASP cc_start: 0.8596 (m-30) cc_final: 0.8220 (m-30)
REVERT: E   24 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8680 (tm-30)
  outliers start: 6
  outliers final: 1
  residues processed: 207
  average time/residue: 0.1159
  time to fit residues: 31.4850
Evaluate side-chains
  151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   45 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
A  31 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 230 ASN
B 293 ASN
B 295 ASN
C  11 GLN
N  77 ASN
R 238 ASN
R 404 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.130212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.098079 restraints weight = 17705.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.100594 restraints weight = 11006.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.101867 restraints weight = 7724.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.102160 restraints weight = 6655.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.102436 restraints weight = 6521.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9453  Z= 0.123
  Angle     :  0.615   9.413  12822  Z= 0.323
  Chirality :  0.042   0.157   1419
  Planarity :  0.005   0.063   1641
  Dihedral  :  5.770  44.437   1285
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.38 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -2.74 (0.23), residues: 1162
  helix: -0.64 (0.24), residues: 422
  sheet: -2.71 (0.29), residues: 234
  loop : -2.32 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 116 
 TYR   0.021   0.001   TYR R 145 
 PHE   0.021   0.001   PHE B 235 
 TRP   0.015   0.001   TRP R 241 
 HIS   0.009   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9447)
  covalent geometry    : angle       0.61417 (12810)
  SS BOND              : bond        0.00559 (    6)
  SS BOND              : angle       1.29777 (   12)
  hydrogen bonds       : bond        0.04024 (  413)
  hydrogen bonds       : angle       5.41030 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.6864 (ttm-80)
REVERT: B  264 TYR cc_start: 0.8252 (m-80) cc_final: 0.7142 (m-80)
REVERT: B  297 TRP cc_start: 0.8620 (m100) cc_final: 0.8417 (m-10)
REVERT: C   51 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (mp)
REVERT: N    5 GLN cc_start: 0.8147 (mp10) cc_final: 0.7792 (mp10)
REVERT: N   38 ARG cc_start: 0.8670 (ptt180) cc_final: 0.8031 (ptt90)
REVERT: N   46 GLU cc_start: 0.6453 (pt0) cc_final: 0.5521 (pt0)
REVERT: N   51 ILE cc_start: 0.8969 (tt) cc_final: 0.8684 (tt)
REVERT: N   76 LYS cc_start: 0.9125 (tppp) cc_final: 0.8316 (tptt)
REVERT: N   91 THR cc_start: 0.8681 (p) cc_final: 0.8476 (p)
REVERT: N  103 PHE cc_start: 0.7778 (m-80) cc_final: 0.7491 (m-80)
REVERT: R  115 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7872 (m-10)
REVERT: R  123 MET cc_start: 0.7697 (mmm) cc_final: 0.7407 (mmm)
REVERT: R  127 GLU cc_start: 0.8553 (mp0) cc_final: 0.7944 (mp0)
REVERT: R  133 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8052 (tp30)
REVERT: R  231 MET cc_start: 0.7724 (tmm) cc_final: 0.7462 (ttp)
REVERT: R  358 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5353 (pt)
REVERT: E   12 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8764 (mtmm)
REVERT: E   17 ARG cc_start: 0.8709 (tpt90) cc_final: 0.8227 (tpp80)
REVERT: E   21 ASP cc_start: 0.8580 (m-30) cc_final: 0.8189 (m-30)
REVERT: E   24 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8691 (tm-30)
REVERT: E   27 MET cc_start: 0.8111 (mmp) cc_final: 0.7702 (mmm)
  outliers start: 21
  outliers final: 13
  residues processed: 215
  average time/residue: 0.1044
  time to fit residues: 29.9791
Evaluate side-chains
  181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  115 TRP
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  358 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 91 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.130267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.098617 restraints weight = 17669.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.100127 restraints weight = 11326.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.101533 restraints weight = 8307.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.102123 restraints weight = 6819.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102339 restraints weight = 6486.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9453  Z= 0.131
  Angle     :  0.598   8.234  12822  Z= 0.314
  Chirality :  0.042   0.153   1419
  Planarity :  0.004   0.061   1641
  Dihedral  :  5.339  34.584   1285
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.87 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.24), residues: 1162
  helix:  0.26 (0.26), residues: 421
  sheet: -2.51 (0.31), residues: 231
  loop : -2.08 (0.27), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 333 
 TYR   0.024   0.001   TYR N  60 
 PHE   0.017   0.001   PHE N 103 
 TRP   0.015   0.001   TRP B 169 
 HIS   0.010   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9447)
  covalent geometry    : angle       0.59731 (12810)
  SS BOND              : bond        0.00503 (    6)
  SS BOND              : angle       1.08996 (   12)
  hydrogen bonds       : bond        0.03669 (  413)
  hydrogen bonds       : angle       4.96719 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 ARG cc_start: 0.7715 (ttm-80) cc_final: 0.7031 (ttm-80)
REVERT: A  317 ARG cc_start: 0.7538 (ptp90) cc_final: 0.7288 (ptp-170)
REVERT: B   82 TRP cc_start: 0.8640 (m100) cc_final: 0.8434 (m100)
REVERT: B  262 MET cc_start: 0.6613 (ttm) cc_final: 0.6373 (ttm)
REVERT: B  264 TYR cc_start: 0.8199 (m-80) cc_final: 0.7495 (m-80)
REVERT: B  297 TRP cc_start: 0.8631 (m100) cc_final: 0.8379 (m-10)
REVERT: C   51 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8543 (mp)
REVERT: N    5 GLN cc_start: 0.8185 (mp10) cc_final: 0.7865 (mp10)
REVERT: N   38 ARG cc_start: 0.8701 (ptt180) cc_final: 0.8069 (ptt90)
REVERT: N   46 GLU cc_start: 0.6542 (pt0) cc_final: 0.5566 (pt0)
REVERT: N   51 ILE cc_start: 0.8957 (tt) cc_final: 0.8569 (tt)
REVERT: N   72 ARG cc_start: 0.8057 (ptm160) cc_final: 0.7146 (ptm160)
REVERT: N   76 LYS cc_start: 0.9114 (tppp) cc_final: 0.8376 (tptt)
REVERT: N   91 THR cc_start: 0.8693 (p) cc_final: 0.8488 (p)
REVERT: R  123 MET cc_start: 0.7842 (mmm) cc_final: 0.7537 (mmm)
REVERT: R  133 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8103 (tp30)
REVERT: E   12 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8806 (mtmm)
REVERT: E   17 ARG cc_start: 0.8685 (tpt90) cc_final: 0.8201 (tpp80)
REVERT: E   21 ASP cc_start: 0.8697 (m-30) cc_final: 0.8293 (m-30)
REVERT: E   24 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8553 (tm-30)
  outliers start: 27
  outliers final: 18
  residues processed: 194
  average time/residue: 0.1054
  time to fit residues: 27.3272
Evaluate side-chains
  170 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   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 213 GLN
A 267 GLN
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.126674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.095778 restraints weight = 17960.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.096404 restraints weight = 11572.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.097223 restraints weight = 9373.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.097806 restraints weight = 8137.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.098170 restraints weight = 7371.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9453  Z= 0.222
  Angle     :  0.668   7.605  12822  Z= 0.347
  Chirality :  0.044   0.158   1419
  Planarity :  0.004   0.058   1641
  Dihedral  :  5.443  35.368   1285
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.31 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.71 (0.25), residues: 1162
  helix:  0.49 (0.26), residues: 422
  sheet: -2.35 (0.31), residues: 229
  loop : -1.89 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG N  72 
 TYR   0.021   0.002   TYR R 145 
 PHE   0.021   0.002   PHE N 108 
 TRP   0.014   0.001   TRP R 241 
 HIS   0.010   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 9447)
  covalent geometry    : angle       0.66706 (12810)
  SS BOND              : bond        0.00394 (    6)
  SS BOND              : angle       1.05705 (   12)
  hydrogen bonds       : bond        0.03789 (  413)
  hydrogen bonds       : angle       4.96051 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 168
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8443 (tttt) cc_final: 0.8181 (mmtm)
REVERT: A  265 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7052 (ttm-80)
REVERT: B   82 TRP cc_start: 0.8698 (m100) cc_final: 0.8323 (m100)
REVERT: B  262 MET cc_start: 0.6912 (ttm) cc_final: 0.6681 (ttm)
REVERT: B  264 TYR cc_start: 0.8330 (m-80) cc_final: 0.7607 (m-80)
REVERT: B  297 TRP cc_start: 0.8696 (m100) cc_final: 0.8489 (m-10)
REVERT: C   51 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8680 (mp)
REVERT: N    5 GLN cc_start: 0.8371 (mp10) cc_final: 0.8023 (mp10)
REVERT: N   38 ARG cc_start: 0.8727 (ptt180) cc_final: 0.8064 (ptt90)
REVERT: N   46 GLU cc_start: 0.6530 (pt0) cc_final: 0.5538 (pt0)
REVERT: N   51 ILE cc_start: 0.9181 (tt) cc_final: 0.8814 (tt)
REVERT: N   72 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7590 (mtp180)
REVERT: N   76 LYS cc_start: 0.9156 (tppp) cc_final: 0.8117 (tptt)
REVERT: N   77 ASN cc_start: 0.8457 (m110) cc_final: 0.8214 (p0)
REVERT: R  123 MET cc_start: 0.7910 (mmm) cc_final: 0.7598 (mmm)
REVERT: R  127 GLU cc_start: 0.8255 (mp0) cc_final: 0.7821 (mp0)
REVERT: R  133 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8195 (tp30)
REVERT: R  270 ILE cc_start: 0.9001 (tt) cc_final: 0.8785 (tt)
REVERT: R  325 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7893 (mt)
REVERT: E    2 SER cc_start: 0.8911 (p) cc_final: 0.8671 (p)
REVERT: E   12 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8855 (mtmm)
REVERT: E   17 ARG cc_start: 0.8738 (tpt90) cc_final: 0.8193 (tpp80)
REVERT: E   21 ASP cc_start: 0.8801 (m-30) cc_final: 0.8381 (m-30)
REVERT: E   24 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8610 (tm-30)
  outliers start: 45
  outliers final: 29
  residues processed: 202
  average time/residue: 0.1017
  time to fit residues: 27.6461
Evaluate side-chains
  186 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  325 ILE
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 110 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0270
   chunk 85 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    1.7244

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 278 ASN
N  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.129196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.096923 restraints weight = 17638.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.099689 restraints weight = 11393.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.101011 restraints weight = 7900.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.100967 restraints weight = 6536.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.101192 restraints weight = 6708.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9453  Z= 0.144
  Angle     :  0.611   9.113  12822  Z= 0.314
  Chirality :  0.042   0.161   1419
  Planarity :  0.004   0.059   1641
  Dihedral  :  5.079  33.902   1285
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 21.95 %
    Favored  : 73.54 %
  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: -1.41 (0.25), residues: 1162
  helix:  0.78 (0.26), residues: 423
  sheet: -2.29 (0.31), residues: 229
  loop : -1.72 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG N  72 
 TYR   0.020   0.001   TYR N  60 
 PHE   0.011   0.001   PHE N 108 
 TRP   0.013   0.001   TRP R 241 
 HIS   0.009   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9447)
  covalent geometry    : angle       0.61101 (12810)
  SS BOND              : bond        0.00438 (    6)
  SS BOND              : angle       0.98152 (   12)
  hydrogen bonds       : bond        0.03421 (  413)
  hydrogen bonds       : angle       4.72386 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 164
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8437 (tttt) cc_final: 0.8179 (mmtm)
REVERT: A  265 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.6968 (ttm-80)
REVERT: A  278 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8285 (m110)
REVERT: A  344 GLU cc_start: 0.8157 (tp30) cc_final: 0.7780 (tp30)
REVERT: B   82 TRP cc_start: 0.8657 (m100) cc_final: 0.8262 (m100)
REVERT: B  264 TYR cc_start: 0.8308 (m-80) cc_final: 0.7609 (m-80)
REVERT: C   51 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8660 (mp)
REVERT: N   38 ARG cc_start: 0.8716 (ptt180) cc_final: 0.8046 (ptt90)
REVERT: N   43 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8006 (mtmm)
REVERT: N   46 GLU cc_start: 0.6528 (pt0) cc_final: 0.5965 (pt0)
REVERT: N   73 ASP cc_start: 0.7975 (t0) cc_final: 0.6468 (t0)
REVERT: N   76 LYS cc_start: 0.9092 (tppp) cc_final: 0.8794 (mtmt)
REVERT: R  123 MET cc_start: 0.7962 (mmm) cc_final: 0.7697 (mmm)
REVERT: R  133 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8158 (tp30)
REVERT: E   12 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8846 (mtmm)
REVERT: E   24 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8660 (tm-30)
  outliers start: 44
  outliers final: 30
  residues processed: 198
  average time/residue: 0.1010
  time to fit residues: 27.0081
Evaluate side-chains
  184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  321 ILE
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 112 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 91 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 43 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.129875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098777 restraints weight = 17715.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.100142 restraints weight = 11969.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.101199 restraints weight = 8326.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.101503 restraints weight = 7484.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.102290 restraints weight = 6802.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9453  Z= 0.139
  Angle     :  0.627   9.860  12822  Z= 0.320
  Chirality :  0.042   0.159   1419
  Planarity :  0.004   0.057   1641
  Dihedral  :  4.931  27.982   1285
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 21.74 %
    Favored  : 74.05 %
  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: -1.19 (0.25), residues: 1162
  helix:  0.96 (0.26), residues: 424
  sheet: -2.07 (0.32), residues: 228
  loop : -1.64 (0.28), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  72 
 TYR   0.018   0.002   TYR N  60 
 PHE   0.011   0.001   PHE N 108 
 TRP   0.015   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9447)
  covalent geometry    : angle       0.62710 (12810)
  SS BOND              : bond        0.00829 (    6)
  SS BOND              : angle       0.67305 (   12)
  hydrogen bonds       : bond        0.03397 (  413)
  hydrogen bonds       : angle       4.62003 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 166
  time to evaluate  : 0.267 
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   28 LYS cc_start: 0.8432 (tttt) cc_final: 0.8169 (mmtm)
REVERT: A  265 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.6971 (ttm110)
REVERT: A  344 GLU cc_start: 0.8070 (tp30) cc_final: 0.7755 (tp30)
REVERT: B   82 TRP cc_start: 0.8652 (m100) cc_final: 0.8250 (m100)
REVERT: B  264 TYR cc_start: 0.8129 (m-80) cc_final: 0.7376 (m-80)
REVERT: C   51 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8668 (mp)
REVERT: N   38 ARG cc_start: 0.8657 (ptt180) cc_final: 0.7962 (ptt90)
REVERT: N   43 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8092 (mtmm)
REVERT: N   46 GLU cc_start: 0.6378 (pt0) cc_final: 0.5685 (pt0)
REVERT: N   68 PHE cc_start: 0.7647 (m-80) cc_final: 0.7419 (m-80)
REVERT: N   73 ASP cc_start: 0.8070 (t0) cc_final: 0.6509 (t0)
REVERT: R  123 MET cc_start: 0.7978 (mmm) cc_final: 0.7680 (mmm)
REVERT: R  131 GLN cc_start: 0.8664 (mm110) cc_final: 0.7779 (tm-30)
REVERT: R  133 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8166 (tp30)
REVERT: E   12 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8862 (mtmm)
  outliers start: 41
  outliers final: 29
  residues processed: 197
  average time/residue: 0.0975
  time to fit residues: 26.1386
Evaluate side-chains
  185 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  321 ILE
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 81 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 104 optimal weight:    0.2980
   chunk 79 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  17 GLN
B 183 HIS
B 237 ASN
B 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.125990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.095002 restraints weight = 17933.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.095642 restraints weight = 11586.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.096403 restraints weight = 9382.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.096998 restraints weight = 8198.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.097402 restraints weight = 7399.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   9453  Z= 0.247
  Angle     :  0.716  13.327  12822  Z= 0.367
  Chirality :  0.046   0.178   1419
  Planarity :  0.005   0.058   1641
  Dihedral  :  5.219  29.252   1283
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 22.87 %
    Favored  : 72.51 %
  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: -1.29 (0.25), residues: 1162
  helix:  0.90 (0.26), residues: 421
  sheet: -2.21 (0.32), residues: 220
  loop : -1.69 (0.28), residues: 521

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG N  72 
 TYR   0.021   0.002   TYR R 145 
 PHE   0.024   0.002   PHE N 108 
 TRP   0.032   0.002   TRP B 297 
 HIS   0.010   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 9447)
  covalent geometry    : angle       0.71587 (12810)
  SS BOND              : bond        0.00338 (    6)
  SS BOND              : angle       1.05298 (   12)
  hydrogen bonds       : bond        0.03759 (  413)
  hydrogen bonds       : angle       4.84106 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 155
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8477 (tttt) cc_final: 0.8211 (mmtm)
REVERT: A  265 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7084 (ttm170)
REVERT: A  344 GLU cc_start: 0.8216 (tp30) cc_final: 0.7941 (tp30)
REVERT: B   82 TRP cc_start: 0.8744 (m100) cc_final: 0.8383 (m100)
REVERT: B  262 MET cc_start: 0.7872 (tmm) cc_final: 0.7650 (tmm)
REVERT: B  264 TYR cc_start: 0.7886 (m-80) cc_final: 0.7474 (m-80)
REVERT: B  311 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8594 (m-70)
REVERT: C   51 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8745 (mp)
REVERT: N   38 ARG cc_start: 0.8760 (ptt180) cc_final: 0.8010 (ptt90)
REVERT: N   46 GLU cc_start: 0.6482 (pt0) cc_final: 0.5744 (pt0)
REVERT: N   51 ILE cc_start: 0.9169 (tt) cc_final: 0.8730 (tt)
REVERT: N   72 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7331 (ptm160)
REVERT: N   76 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8481 (tptt)
REVERT: R  123 MET cc_start: 0.8004 (mmm) cc_final: 0.7703 (mmm)
REVERT: R  131 GLN cc_start: 0.8795 (mm110) cc_final: 0.7962 (tm-30)
REVERT: R  133 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8173 (tp30)
REVERT: R  231 MET cc_start: 0.7928 (tmm) cc_final: 0.7481 (ttp)
REVERT: R  270 ILE cc_start: 0.9074 (tt) cc_final: 0.8851 (tt)
REVERT: R  317 ILE cc_start: 0.8724 (tp) cc_final: 0.8363 (tt)
REVERT: E    2 SER cc_start: 0.8944 (p) cc_final: 0.8670 (p)
REVERT: E   12 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8883 (mtmm)
  outliers start: 45
  outliers final: 34
  residues processed: 190
  average time/residue: 0.0924
  time to fit residues: 24.0909
Evaluate side-chains
  184 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 148
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  316 LEU
Chi-restraints excluded: chain R residue  321 ILE
Chi-restraints excluded: chain R residue  323 VAL
Chi-restraints excluded: chain R residue  328 LEU
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B  17 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.131001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.099685 restraints weight = 17445.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.101118 restraints weight = 11132.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.102714 restraints weight = 8221.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.103486 restraints weight = 6638.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.103823 restraints weight = 6458.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   9453  Z= 0.123
  Angle     :  0.656  12.988  12822  Z= 0.328
  Chirality :  0.042   0.160   1419
  Planarity :  0.004   0.055   1641
  Dihedral  :  4.792  26.839   1283
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 24.21 %
    Favored  : 72.21 %
  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 (0.25), residues: 1162
  helix:  1.10 (0.26), residues: 426
  sheet: -2.05 (0.32), residues: 229
  loop : -1.47 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  72 
 TYR   0.017   0.001   TYR R 145 
 PHE   0.012   0.001   PHE R 230 
 TRP   0.022   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9447)
  covalent geometry    : angle       0.65533 (12810)
  SS BOND              : bond        0.00445 (    6)
  SS BOND              : angle       0.92503 (   12)
  hydrogen bonds       : bond        0.03271 (  413)
  hydrogen bonds       : angle       4.59537 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 167
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8261 (m110)
REVERT: A  344 GLU cc_start: 0.8116 (tp30) cc_final: 0.7805 (tp30)
REVERT: B   82 TRP cc_start: 0.8666 (m100) cc_final: 0.8274 (m100)
REVERT: B  262 MET cc_start: 0.7856 (tmm) cc_final: 0.7642 (tmm)
REVERT: C   51 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8630 (mp)
REVERT: N   38 ARG cc_start: 0.8710 (ptt180) cc_final: 0.7934 (ptt90)
REVERT: N   43 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8132 (mtmm)
REVERT: N   46 GLU cc_start: 0.6412 (pt0) cc_final: 0.5640 (pt0)
REVERT: N   72 ARG cc_start: 0.7812 (ptm160) cc_final: 0.7525 (ptm160)
REVERT: N   76 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8261 (tptt)
REVERT: R  123 MET cc_start: 0.8012 (mmm) cc_final: 0.7757 (mmm)
REVERT: R  131 GLN cc_start: 0.8696 (mm110) cc_final: 0.7754 (tm-30)
REVERT: R  133 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8205 (tp30)
REVERT: R  231 MET cc_start: 0.7722 (tmm) cc_final: 0.7250 (ttp)
REVERT: R  297 SER cc_start: 0.8839 (m) cc_final: 0.8571 (t)
REVERT: R  317 ILE cc_start: 0.8432 (tp) cc_final: 0.8171 (tt)
REVERT: E    2 SER cc_start: 0.8968 (p) cc_final: 0.8703 (p)
REVERT: E   12 LYS cc_start: 0.9239 (mtmt) cc_final: 0.8834 (mtmm)
  outliers start: 35
  outliers final: 26
  residues processed: 193
  average time/residue: 0.0985
  time to fit residues: 25.9124
Evaluate side-chains
  176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue   67 CYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  323 VAL
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  363 VAL
Chi-restraints excluded: chain R residue  399 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 104 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.131092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.099823 restraints weight = 17445.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.100752 restraints weight = 11178.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.102278 restraints weight = 8707.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.104086 restraints weight = 6873.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.104345 restraints weight = 6111.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   9453  Z= 0.139
  Angle     :  0.681  15.116  12822  Z= 0.340
  Chirality :  0.043   0.151   1419
  Planarity :  0.004   0.055   1641
  Dihedral  :  4.766  25.564   1283
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 25.33 %
    Favored  : 71.18 %
  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: -0.97 (0.25), residues: 1162
  helix:  1.13 (0.26), residues: 426
  sheet: -2.02 (0.32), residues: 232
  loop : -1.46 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 214 
 TYR   0.017   0.001   TYR R 145 
 PHE   0.011   0.001   PHE B 235 
 TRP   0.019   0.001   TRP B 297 
 HIS   0.009   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9447)
  covalent geometry    : angle       0.68060 (12810)
  SS BOND              : bond        0.00423 (    6)
  SS BOND              : angle       0.97742 (   12)
  hydrogen bonds       : bond        0.03329 (  413)
  hydrogen bonds       : angle       4.57226 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8421 (tttt) cc_final: 0.8191 (mmtm)
REVERT: A  265 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.6932 (ttm-80)
REVERT: A  344 GLU cc_start: 0.8201 (tp30) cc_final: 0.7904 (tp30)
REVERT: B   82 TRP cc_start: 0.8685 (m100) cc_final: 0.8299 (m100)
REVERT: B  294 CYS cc_start: 0.8531 (p) cc_final: 0.8302 (p)
REVERT: C   51 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8642 (mp)
REVERT: N   32 TYR cc_start: 0.8276 (m-10) cc_final: 0.7852 (m-10)
REVERT: N   38 ARG cc_start: 0.8725 (ptt180) cc_final: 0.7939 (ptt90)
REVERT: N   43 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8171 (mtmm)
REVERT: N   46 GLU cc_start: 0.6406 (pt0) cc_final: 0.5663 (pt0)
REVERT: N   76 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8289 (tptt)
REVERT: R  123 MET cc_start: 0.8030 (mmm) cc_final: 0.7778 (mmm)
REVERT: R  131 GLN cc_start: 0.8708 (mm110) cc_final: 0.7800 (tm-30)
REVERT: R  133 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8142 (tp30)
REVERT: R  231 MET cc_start: 0.7806 (tmm) cc_final: 0.7355 (ttp)
REVERT: R  297 SER cc_start: 0.8853 (m) cc_final: 0.8580 (t)
REVERT: E   12 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8827 (mtmm)
  outliers start: 34
  outliers final: 24
  residues processed: 180
  average time/residue: 0.0990
  time to fit residues: 24.1841
Evaluate side-chains
  178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain B residue  339 TRP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  323 VAL
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.129732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.098924 restraints weight = 17665.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.099480 restraints weight = 11992.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.101002 restraints weight = 9367.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.101475 restraints weight = 7335.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.101876 restraints weight = 7040.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   9453  Z= 0.169
  Angle     :  0.711  14.935  12822  Z= 0.355
  Chirality :  0.044   0.155   1419
  Planarity :  0.004   0.054   1641
  Dihedral  :  4.875  25.953   1283
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.74 %
    Favored  : 71.08 %
  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: -0.94 (0.25), residues: 1162
  helix:  1.08 (0.26), residues: 428
  sheet: -1.93 (0.33), residues: 218
  loop : -1.46 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 214 
 TYR   0.018   0.002   TYR R 145 
 PHE   0.019   0.001   PHE R 230 
 TRP   0.028   0.001   TRP B 297 
 HIS   0.012   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 9447)
  covalent geometry    : angle       0.71033 (12810)
  SS BOND              : bond        0.00413 (    6)
  SS BOND              : angle       0.95881 (   12)
  hydrogen bonds       : bond        0.03376 (  413)
  hydrogen bonds       : angle       4.64759 ( 1197)

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 156
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LYS cc_start: 0.8439 (tttt) cc_final: 0.8211 (mmtm)
REVERT: A  265 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7016 (ttm-80)
REVERT: A  278 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.8235 (m110)
REVERT: A  344 GLU cc_start: 0.8156 (tp30) cc_final: 0.7904 (tp30)
REVERT: B   82 TRP cc_start: 0.8680 (m100) cc_final: 0.8278 (m100)
REVERT: B  264 TYR cc_start: 0.7318 (m-80) cc_final: 0.6748 (m-80)
REVERT: B  294 CYS cc_start: 0.8469 (p) cc_final: 0.8261 (p)
REVERT: C   51 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8678 (mp)
REVERT: N   38 ARG cc_start: 0.8725 (ptt180) cc_final: 0.7961 (ptt90)
REVERT: N   43 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8316 (mtmm)
REVERT: N   46 GLU cc_start: 0.6415 (pt0) cc_final: 0.5667 (pt0)
REVERT: N   76 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8353 (tptt)
REVERT: N   82 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7204 (mp10)
REVERT: R  123 MET cc_start: 0.8085 (mmm) cc_final: 0.7804 (mmm)
REVERT: R  131 GLN cc_start: 0.8762 (mm110) cc_final: 0.7876 (tm-30)
REVERT: R  133 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8166 (tp30)
REVERT: R  230 PHE cc_start: 0.8533 (t80) cc_final: 0.8291 (t80)
REVERT: R  231 MET cc_start: 0.7962 (tmm) cc_final: 0.7423 (ttp)
REVERT: R  297 SER cc_start: 0.8880 (m) cc_final: 0.8601 (t)
REVERT: E   12 LYS cc_start: 0.9250 (mtmt) cc_final: 0.8839 (mtmm)
  outliers start: 31
  outliers final: 24
  residues processed: 179
  average time/residue: 0.0969
  time to fit residues: 23.8274
Evaluate side-chains
  177 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   57 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  311 TYR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain N residue   43 LYS
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain R residue   64 LYS
Chi-restraints excluded: chain R residue   65 TYR
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  147 VAL
Chi-restraints excluded: chain R residue  193 VAL
Chi-restraints excluded: chain R residue  206 ILE
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  279 VAL
Chi-restraints excluded: chain R residue  323 VAL
Chi-restraints excluded: chain R residue  330 VAL
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  363 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 68 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 58 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.129779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.099389 restraints weight = 17478.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.099763 restraints weight = 11074.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.100980 restraints weight = 9226.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.101684 restraints weight = 7212.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.101798 restraints weight = 6671.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.159   9453  Z= 0.207
  Angle     :  1.007  59.198  12822  Z= 0.577
  Chirality :  0.051   1.053   1419
  Planarity :  0.004   0.053   1641
  Dihedral  :  4.985  39.446   1283
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.25 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.15 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.95 (0.25), residues: 1162
  helix:  1.06 (0.26), residues: 428
  sheet: -1.91 (0.33), residues: 218
  loop : -1.46 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 214 
 TYR   0.018   0.001   TYR R 145 
 PHE   0.059   0.002   PHE N  68 
 TRP   0.023   0.001   TRP B 297 
 HIS   0.009   0.001   HIS R 361 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 9447)
  covalent geometry    : angle       1.00680 (12810)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       0.94029 (   12)
  hydrogen bonds       : bond        0.03690 (  413)
  hydrogen bonds       : angle       4.70589 ( 1197)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1545.05 seconds
wall clock time: 27 minutes 26.66 seconds (1646.66 seconds total)