Starting phenix.real_space_refine
on Thu Mar 13 21:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2025/7vbi_31880.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.108
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      54      5.16       5
     C    5882      2.51       5
     N    1596      2.21       5
     O    1691      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9223
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1891
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 6, 'TRANS': 220}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "P"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 229
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'AIB:plan-1': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "R"
      Number of atoms: 3115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3115
          Classifications: {'peptide': 382}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 13, 'TRANS': 368}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2591
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
  Time building chain proxies: 5.02, per 1000 atoms: 0.54
  Number of scatterers: 9223
  At special positions: 0
  Unit cell: (76.041, 100.674, 173.502, 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      54     16.00
     O    1691      8.00
     N    1596      7.00
     C    5882      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=2.04
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.02

  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: 2.68
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2178

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      40.8% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 38
      removed outlier: 3.547A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
      removed outlier: 3.758A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 238
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.565A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.646A  pdb=" N   ALA A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.416A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 3.833A  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 350
      removed outlier: 3.912A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 337 " --> pdb=" O   ARG A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
    Processing helix  chain 'P' and resid 2 through 29
      removed outlier: 3.669A  pdb=" N   VAL P  23 " --> pdb=" O   GLN P  19 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA P  28 " --> pdb=" O   GLN P  24 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 51
      removed outlier: 3.577A  pdb=" N   TYR R  42 " --> pdb=" O   LYS R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 169
      removed outlier: 3.583A  pdb=" N   PHE R 169 " --> pdb=" O   ILE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 205
      removed outlier: 3.725A  pdb=" N   PHE R 195 " --> pdb=" O   ALA R 191 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   TYR R 205 " --> pdb=" O   LEU R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 214
    Processing helix  chain 'R' and resid 219 through 222
    Processing helix  chain 'R' and resid 223 through 256
      removed outlier: 4.037A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL R 237 " --> pdb=" O   MET R 233 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA R 238 " --> pdb=" O   GLN R 234 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASN R 240 " --> pdb=" O   CYS R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 275
      removed outlier: 3.761A  pdb=" N   SER R 271 " --> pdb=" O   ARG R 267 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 280
      removed outlier: 3.786A  pdb=" N   PHE R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 291
    Processing helix  chain 'R' and resid 293 through 298
      removed outlier: 4.496A  pdb=" N   CYS R 296 " --> pdb=" O   ASP R 293 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP R 297 " --> pdb=" O   GLU R 294 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 306 through 336
      Proline residue:  R 312  - end of helix
      removed outlier: 3.663A  pdb=" N   ALA R 316 " --> pdb=" O   PRO R 312 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   CYS R 329 " --> pdb=" O   VAL R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 346 through 361
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 377 through 389
    Processing helix  chain 'R' and resid 390 through 403
      removed outlier: 3.635A  pdb=" N   GLY R 395 " --> pdb=" O   THR R 391 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LEU R 396 " --> pdb=" O   SER R 392 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 422
      removed outlier: 3.962A  pdb=" N   GLU R 412 " --> pdb=" O   GLU R 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.877A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 4.006A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 22
      removed outlier: 3.794A  pdb=" N   GLN G  18 " --> pdb=" O   LYS G  14 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.521A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.185A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.626A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.454A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'R' and resid 82 through 83
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.573A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.670A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.928A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.698A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.996A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.351A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 278
      removed outlier: 4.063A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1221 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: 2.65

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2583
        1.33 -     1.46: 2487
        1.46 -     1.58: 4288
        1.58 -     1.71: 0
        1.71 -     1.84: 73
  Bond restraints: 9431
  Sorted by residual:
  bond pdb=" C   PHE B 234 "
       pdb=" N   PHE B 235 "
    ideal  model  delta    sigma   weight residual
    1.328  1.274  0.054 1.44e-02 4.82e+03 1.41e+01
  bond pdb=" CA  PHE A 238 "
       pdb=" CB  PHE A 238 "
    ideal  model  delta    sigma   weight residual
    1.526  1.471  0.055 1.51e-02 4.39e+03 1.33e+01
  bond pdb=" CG1 ILE B  81 "
       pdb=" CD1 ILE B  81 "
    ideal  model  delta    sigma   weight residual
    1.513  1.398  0.115 3.90e-02 6.57e+02 8.62e+00
  bond pdb=" C   PHE B 235 "
       pdb=" N   PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.19e-02 7.06e+03 7.67e+00
  bond pdb=" CG1 ILE B  58 "
       pdb=" CD1 ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.410  0.103 3.90e-02 6.57e+02 6.91e+00
  ... (remaining 9426 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 12321
        2.56 -     5.12: 400
        5.12 -     7.69: 48
        7.69 -    10.25: 12
       10.25 -    12.81: 6
  Bond angle restraints: 12787
  Sorted by residual:
  angle pdb=" C   THR A 319 "
        pdb=" N   THR A 320 "
        pdb=" CA  THR A 320 "
      ideal   model   delta    sigma   weight residual
     120.51  130.15   -9.64 1.45e+00 4.76e-01 4.42e+01
  angle pdb=" O   ASP B 291 "
        pdb=" C   ASP B 291 "
        pdb=" N   PHE B 292 "
      ideal   model   delta    sigma   weight residual
     122.39  129.37   -6.98 1.29e+00 6.01e-01 2.93e+01
  angle pdb=" C   PHE B 234 "
        pdb=" N   PHE B 235 "
        pdb=" CA  PHE B 235 "
      ideal   model   delta    sigma   weight residual
     120.39  127.58   -7.19 1.39e+00 5.18e-01 2.67e+01
  angle pdb=" C   ARG N  98 "
        pdb=" N   CYS N  99 "
        pdb=" CA  CYS N  99 "
      ideal   model   delta    sigma   weight residual
     122.74  110.14   12.60 2.44e+00 1.68e-01 2.67e+01
  angle pdb=" N   VAL R 405 "
        pdb=" CA  VAL R 405 "
        pdb=" C   VAL R 405 "
      ideal   model   delta    sigma   weight residual
     113.10  108.34    4.76 9.70e-01 1.06e+00 2.41e+01
  ... (remaining 12782 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.13: 4972
       18.13 -    36.25: 488
       36.25 -    54.38: 83
       54.38 -    72.50: 21
       72.50 -    90.63: 9
  Dihedral angle restraints: 5573
    sinusoidal: 2202
      harmonic: 3371
  Sorted by residual:
  dihedral pdb=" CB  CYS R  85 "
           pdb=" SG  CYS R  85 "
           pdb=" SG  CYS R 126 "
           pdb=" CB  CYS R 126 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.50  -69.50     1      1.00e+01 1.00e-02 6.24e+01
  dihedral pdb=" CA  CYS N  99 "
           pdb=" C   CYS N  99 "
           pdb=" N   PRO N 100 "
           pdb=" CA  PRO N 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.63  -35.37     0      5.00e+00 4.00e-02 5.00e+01
  dihedral pdb=" CA  LEU R 217 "
           pdb=" C   LEU R 217 "
           pdb=" N   LEU R 218 "
           pdb=" CA  LEU R 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.84   33.16     0      5.00e+00 4.00e-02 4.40e+01
  ... (remaining 5570 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 873
       0.050 -    0.101: 396
       0.101 -    0.151: 110
       0.151 -    0.201: 23
       0.201 -    0.251: 10
  Chirality restraints: 1412
  Sorted by residual:
  chirality pdb=" CB  ILE N  51 "
            pdb=" CA  ILE N  51 "
            pdb=" CG1 ILE N  51 "
            pdb=" CG2 ILE N  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  ILE A 308 "
            pdb=" CA  ILE A 308 "
            pdb=" CG1 ILE A 308 "
            pdb=" CG2 ILE A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  VAL R 282 "
            pdb=" N   VAL R 282 "
            pdb=" C   VAL R 282 "
            pdb=" CB  VAL R 282 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.21    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1409 not shown)

  Planarity restraints: 1623
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 384 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   LEU R 384 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   LEU R 384 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PHE R 385 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  55 "   -0.051 5.00e-02 4.00e+02   7.55e-02 9.12e+00
        pdb=" N   PRO R  56 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO R  56 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO R  56 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 395 "   -0.015 2.00e-02 2.50e+03   2.95e-02 8.71e+00
        pdb=" C   GLY R 395 "    0.051 2.00e-02 2.50e+03
        pdb=" O   GLY R 395 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU R 396 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1620 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 745
        2.73 -     3.27: 8443
        3.27 -     3.81: 14905
        3.81 -     4.36: 18454
        4.36 -     4.90: 32142
  Nonbonded interactions: 74689
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   TYR R  69 "
            pdb=" OH  TYR R  88 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NE2 HIS A 362 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OE2 GLU P   3 "
            pdb=" OH  TYR R 152 "
     model   vdw
     2.315 3.040
  ... (remaining 74684 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.630
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
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      :  0.011   0.115   9431  Z= 0.738
  Angle     :  1.125  12.808  12787  Z= 0.633
  Chirality :  0.063   0.251   1412
  Planarity :  0.008   0.076   1623
  Dihedral  : 14.914  90.630   3377
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.42 %
    Favored  : 91.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.06 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.46 (0.20), residues: 1133
  helix: -2.64 (0.18), residues: 429
  sheet: -1.08 (0.32), residues: 229
  loop : -2.44 (0.23), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP R  72 
 HIS   0.020   0.003   HIS A 357 
 PHE   0.044   0.004   PHE N 108 
 TYR   0.027   0.003   TYR R 148 
 ARG   0.014   0.001   ARG B   8 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 1.038 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8286 (mt) cc_final: 0.8052 (mm)
REVERT: A  339 TYR cc_start: 0.8678 (m-80) cc_final: 0.8439 (m-80)
REVERT: N   34 MET cc_start: 0.8108 (mmm) cc_final: 0.7733 (mmm)
REVERT: N   46 GLU cc_start: 0.7187 (mp0) cc_final: 0.6890 (mp0)
REVERT: N   94 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80)
REVERT: N   95 TYR cc_start: 0.8513 (m-80) cc_final: 0.8165 (m-80)
REVERT: P    9 ASP cc_start: 0.8069 (m-30) cc_final: 0.7473 (m-30)
REVERT: R  146 ILE cc_start: 0.8759 (mt) cc_final: 0.8484 (mp)
REVERT: R  267 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6324 (mpp80)
REVERT: R  336 LYS cc_start: 0.8081 (mttp) cc_final: 0.7778 (mmtm)
REVERT: R  348 ARG cc_start: 0.7395 (tpm170) cc_final: 0.6602 (mtp180)
REVERT: R  376 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7274 (mtt90)
REVERT: R  415 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6697 (mttt)
REVERT: B   42 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7059 (ttm-80)
  outliers start: 8
  outliers final: 4
  residues processed: 177
  average time/residue: 1.4128
  time to fit residues: 266.0303
Evaluate side-chains
  135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0570
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:   20.0000
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
A  35 GLN
A 227 GLN
A 279 ASN
A 371 ASN
N   1 GLN
N  31 ASN
N  77 ASN
R  37 GLN
R  45 GLN
R 140 GLN
R 211 GLN
R 221 GLN
B 119 ASN
B 132 ASN
B 230 ASN
B 239 ASN
G  24 ASN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.193054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149243 restraints weight = 10073.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.74
r_work: 0.3323 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   9431  Z= 0.202
  Angle     :  0.608   8.982  12787  Z= 0.327
  Chirality :  0.041   0.150   1412
  Planarity :  0.005   0.062   1623
  Dihedral  :  5.867  50.026   1273
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.72 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.23), residues: 1133
  helix: -0.50 (0.24), residues: 433
  sheet: -0.52 (0.32), residues: 242
  loop : -2.04 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 214 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.022   0.001   TYR R 148 
 ARG   0.007   0.000   ARG A 283 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 147
  time to evaluate  : 1.404 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8367 (mt) cc_final: 0.8114 (mm)
REVERT: A  283 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7533 (mtm110)
REVERT: A  347 ARG cc_start: 0.7808 (ttp-170) cc_final: 0.7580 (ttp80)
REVERT: N   34 MET cc_start: 0.8467 (mmm) cc_final: 0.8076 (mmm)
REVERT: N   39 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8008 (tt0)
REVERT: N   46 GLU cc_start: 0.8191 (mp0) cc_final: 0.7951 (mp0)
REVERT: P    3 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7108 (mm-30)
REVERT: R  146 ILE cc_start: 0.8806 (mt) cc_final: 0.8582 (mp)
REVERT: R  167 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7677 (pp)
REVERT: R  202 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7463 (tttp)
REVERT: R  267 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6347 (mpp80)
REVERT: R  336 LYS cc_start: 0.7862 (mttp) cc_final: 0.7594 (mmtm)
REVERT: R  376 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.6984 (mtt90)
REVERT: R  387 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5829 (mt-10)
REVERT: B   42 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6769 (ttm-80)
REVERT: B  217 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7835 (pmm)
REVERT: G   21 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4984 (tmm)
  outliers start: 37
  outliers final: 14
  residues processed: 165
  average time/residue: 1.3929
  time to fit residues: 244.5447
Evaluate side-chains
  157 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  271 SER
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 63 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 86 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
A 279 ASN
A 387 HIS
N  31 ASN
N  77 ASN
R  37 GLN
** R  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 394 GLN
B 230 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.187954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.135338 restraints weight = 10237.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.41
r_work: 0.3316 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   9431  Z= 0.293
  Angle     :  0.634  10.345  12787  Z= 0.337
  Chirality :  0.043   0.204   1412
  Planarity :  0.005   0.061   1623
  Dihedral  :  5.633  40.048   1269
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.35 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.24), residues: 1133
  helix:  0.27 (0.25), residues: 433
  sheet: -0.48 (0.32), residues: 242
  loop : -2.00 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 214 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.017   0.002   PHE N 108 
 TYR   0.023   0.002   TYR R 148 
 ARG   0.008   0.000   ARG R  44 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.8392 (mt) cc_final: 0.8163 (mp)
REVERT: A  283 ARG cc_start: 0.7931 (ptp-110) cc_final: 0.7601 (mtm110)
REVERT: A  308 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: A  356 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6928 (mtm110)
REVERT: A  386 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8363 (ttm)
REVERT: N   34 MET cc_start: 0.8616 (mmm) cc_final: 0.8224 (mmm)
REVERT: N   39 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8167 (tt0)
REVERT: N   46 GLU cc_start: 0.8573 (mp0) cc_final: 0.8270 (mp0)
REVERT: N   95 TYR cc_start: 0.8648 (m-80) cc_final: 0.8430 (m-80)
REVERT: P    3 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7108 (mm-30)
REVERT: R   44 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8174 (ttp80)
REVERT: R  146 ILE cc_start: 0.8855 (mt) cc_final: 0.8612 (mp)
REVERT: R  167 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7554 (pp)
REVERT: R  202 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7431 (tttp)
REVERT: R  267 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6231 (mpp80)
REVERT: R  336 LYS cc_start: 0.7797 (mttp) cc_final: 0.7414 (mmtm)
REVERT: R  348 ARG cc_start: 0.7475 (tpm-80) cc_final: 0.6215 (mtp180)
REVERT: R  376 ARG cc_start: 0.7796 (ptp-170) cc_final: 0.7103 (mtt90)
REVERT: R  387 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6039 (mt-10)
REVERT: B   42 ARG cc_start: 0.7671 (ttp-110) cc_final: 0.7003 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8790 (pt)
REVERT: B  171 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8552 (mm)
REVERT: B  217 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7710 (pmm)
REVERT: G   21 MET cc_start: 0.5165 (tmt) cc_final: 0.4869 (tmm)
  outliers start: 40
  outliers final: 17
  residues processed: 163
  average time/residue: 1.3105
  time to fit residues: 227.4620
Evaluate side-chains
  155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  172 GLU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0970
   chunk 90 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 43 optimal weight:   30.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
R  37 GLN
B 230 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 = 0.4131 r_free = 0.4131 target = 0.189552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.135556 restraints weight = 10124.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.52
r_work: 0.3310 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9431  Z= 0.199
  Angle     :  0.562   6.757  12787  Z= 0.300
  Chirality :  0.041   0.146   1412
  Planarity :  0.004   0.062   1623
  Dihedral  :  5.213  37.253   1269
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.07 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.24), residues: 1133
  helix:  0.73 (0.25), residues: 436
  sheet: -0.11 (0.33), residues: 234
  loop : -1.86 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 214 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.018   0.001   TYR R 148 
 ARG   0.005   0.000   ARG R  44 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 144
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.8201 (mt) cc_final: 0.7955 (mp)
REVERT: A  283 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.7353 (mtm110)
REVERT: A  308 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: A  356 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6917 (mtm110)
REVERT: A  386 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8167 (ttm)
REVERT: N   34 MET cc_start: 0.8411 (mmm) cc_final: 0.8039 (mmm)
REVERT: N   46 GLU cc_start: 0.8339 (mp0) cc_final: 0.7939 (mp0)
REVERT: P    3 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6841 (mm-30)
REVERT: R  146 ILE cc_start: 0.8760 (mt) cc_final: 0.8527 (mp)
REVERT: R  202 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7313 (tptp)
REVERT: R  267 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6202 (mpp80)
REVERT: R  336 LYS cc_start: 0.7673 (mttp) cc_final: 0.7291 (mmtm)
REVERT: R  348 ARG cc_start: 0.7318 (tpm-80) cc_final: 0.6124 (mtp180)
REVERT: R  364 GLU cc_start: 0.7805 (mp0) cc_final: 0.7388 (mp0)
REVERT: R  376 ARG cc_start: 0.7542 (ptp-170) cc_final: 0.6872 (mmt90)
REVERT: R  387 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5849 (mt-10)
REVERT: B   42 ARG cc_start: 0.7518 (ttp-110) cc_final: 0.7071 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: B  100 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8828 (p)
REVERT: B  217 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7671 (pmm)
REVERT: G   21 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4723 (tmm)
  outliers start: 42
  outliers final: 18
  residues processed: 169
  average time/residue: 1.2228
  time to fit residues: 220.7597
Evaluate side-chains
  158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 82 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 239 ASN
A 279 ASN
N  77 ASN
B  75 GLN
B 230 ASN
B 239 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.189761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.130387 restraints weight = 10219.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.29
r_work: 0.3263 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9431  Z= 0.293
  Angle     :  0.609   8.739  12787  Z= 0.322
  Chirality :  0.043   0.157   1412
  Planarity :  0.004   0.063   1623
  Dihedral  :  5.296  37.243   1269
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.80 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.24), residues: 1133
  helix:  0.87 (0.25), residues: 437
  sheet:  0.01 (0.33), residues: 229
  loop : -1.78 (0.26), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.022   0.002   PHE N 108 
 TYR   0.022   0.002   TYR R 148 
 ARG   0.008   0.000   ARG R  44 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 134
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 LEU cc_start: 0.8352 (mt) cc_final: 0.8130 (mp)
REVERT: A  283 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7372 (mtm110)
REVERT: A  308 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7679 (tp)
REVERT: A  356 ARG cc_start: 0.7096 (mtm110) cc_final: 0.6849 (mtm110)
REVERT: A  386 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8171 (ttm)
REVERT: N   34 MET cc_start: 0.8403 (mmm) cc_final: 0.8098 (mmm)
REVERT: N   39 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8019 (tt0)
REVERT: N   79 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7097 (tp)
REVERT: P    3 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6865 (mm-30)
REVERT: R   44 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7904 (ttp80)
REVERT: R  146 ILE cc_start: 0.8824 (mt) cc_final: 0.8598 (mp)
REVERT: R  202 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7460 (tttp)
REVERT: R  267 ARG cc_start: 0.7273 (tpt170) cc_final: 0.6311 (mpp80)
REVERT: R  303 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7896 (mtt)
REVERT: R  336 LYS cc_start: 0.7773 (mttp) cc_final: 0.7387 (mmtm)
REVERT: R  348 ARG cc_start: 0.7438 (tpm-80) cc_final: 0.6213 (mtp180)
REVERT: R  376 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7088 (mtt90)
REVERT: R  387 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6037 (mt-10)
REVERT: R  418 GLU cc_start: 0.7064 (tp30) cc_final: 0.6763 (tm-30)
REVERT: B   42 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7176 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8779 (pt)
REVERT: B  100 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8898 (p)
REVERT: B  171 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8399 (mm)
REVERT: B  217 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (pmm)
REVERT: G   21 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.4830 (tmm)
  outliers start: 45
  outliers final: 19
  residues processed: 161
  average time/residue: 1.5076
  time to fit residues: 259.1827
Evaluate side-chains
  154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  100 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  194 VAL
Chi-restraints excluded: chain R residue  198 ASP
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  303 MET
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain G residue   21 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.0270
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 279 ASN
N  77 ASN
R 112 GLN
B 239 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.191849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.134715 restraints weight = 10058.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.69
r_work: 0.3279 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9431  Z= 0.175
  Angle     :  0.562   8.500  12787  Z= 0.299
  Chirality :  0.041   0.151   1412
  Planarity :  0.004   0.065   1623
  Dihedral  :  5.069  37.211   1269
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.92 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 1133
  helix:  1.09 (0.25), residues: 442
  sheet:  0.21 (0.34), residues: 229
  loop : -1.74 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE N 108 
 TYR   0.019   0.001   TYR N  95 
 ARG   0.004   0.000   ARG B 197 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 135
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8261 (mt) cc_final: 0.8007 (mp)
REVERT: A  283 ARG cc_start: 0.7648 (ptp-110) cc_final: 0.7278 (mtm110)
REVERT: A  308 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7474 (mt)
REVERT: A  356 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6855 (mtm110)
REVERT: A  392 GLU cc_start: 0.7874 (mp0) cc_final: 0.7610 (mm-30)
REVERT: N   34 MET cc_start: 0.8414 (mmm) cc_final: 0.8042 (mmm)
REVERT: N   39 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7990 (tt0)
REVERT: N   46 GLU cc_start: 0.8311 (mp0) cc_final: 0.8020 (mp0)
REVERT: N   79 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6992 (tp)
REVERT: P    3 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6824 (mm-30)
REVERT: R   41 GLU cc_start: 0.8344 (pp20) cc_final: 0.7684 (pp20)
REVERT: R   68 GLU cc_start: 0.5218 (tt0) cc_final: 0.4899 (tt0)
REVERT: R  146 ILE cc_start: 0.8763 (mt) cc_final: 0.8506 (mp)
REVERT: R  267 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6272 (mpp80)
REVERT: R  336 LYS cc_start: 0.7671 (mttp) cc_final: 0.7267 (mmtm)
REVERT: R  348 ARG cc_start: 0.7336 (tpm-80) cc_final: 0.6090 (mtp180)
REVERT: R  376 ARG cc_start: 0.7478 (ptp-170) cc_final: 0.6818 (mtt90)
REVERT: R  387 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5913 (mt-10)
REVERT: R  418 GLU cc_start: 0.6969 (tp30) cc_final: 0.6671 (tm-30)
REVERT: B   42 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7107 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8621 (pt)
REVERT: B  100 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (p)
REVERT: B  171 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8340 (mm)
REVERT: B  217 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7695 (pmm)
  outliers start: 43
  outliers final: 15
  residues processed: 161
  average time/residue: 1.2935
  time to fit residues: 223.6398
Evaluate side-chains
  150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 76 optimal weight:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 88 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
R  37 GLN
R  45 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.190938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.133656 restraints weight = 10188.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.65
r_work: 0.3268 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9431  Z= 0.201
  Angle     :  0.563   7.967  12787  Z= 0.299
  Chirality :  0.041   0.168   1412
  Planarity :  0.004   0.065   1623
  Dihedral  :  4.988  40.838   1269
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.44 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.25), residues: 1133
  helix:  1.31 (0.26), residues: 438
  sheet:  0.30 (0.34), residues: 234
  loop : -1.66 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.019   0.001   PHE B 292 
 TYR   0.018   0.001   TYR N  95 
 ARG   0.004   0.000   ARG B 197 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8272 (mt) cc_final: 0.8040 (mp)
REVERT: A  283 ARG cc_start: 0.7682 (ptp-110) cc_final: 0.7309 (mtm110)
REVERT: A  308 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7525 (mt)
REVERT: A  356 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6865 (mtm110)
REVERT: A  392 GLU cc_start: 0.7851 (mp0) cc_final: 0.7622 (mm-30)
REVERT: N   34 MET cc_start: 0.8402 (mmm) cc_final: 0.8051 (mmm)
REVERT: N   39 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8013 (tt0)
REVERT: N   46 GLU cc_start: 0.8340 (mp0) cc_final: 0.8049 (mp0)
REVERT: N   79 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: P    3 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6847 (mm-30)
REVERT: R   41 GLU cc_start: 0.8420 (pp20) cc_final: 0.8027 (pp20)
REVERT: R  146 ILE cc_start: 0.8768 (mt) cc_final: 0.8477 (mp)
REVERT: R  267 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6301 (mpp80)
REVERT: R  336 LYS cc_start: 0.7661 (mttp) cc_final: 0.7349 (mmtm)
REVERT: R  348 ARG cc_start: 0.7357 (tpm-80) cc_final: 0.6131 (mtp180)
REVERT: R  376 ARG cc_start: 0.7420 (ptp-170) cc_final: 0.6797 (mtt90)
REVERT: R  387 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.5915 (mt-10)
REVERT: R  418 GLU cc_start: 0.6998 (tp30) cc_final: 0.6690 (tm-30)
REVERT: B   42 ARG cc_start: 0.7611 (ttp-110) cc_final: 0.7143 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8650 (pt)
REVERT: B  100 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (p)
REVERT: B  134 ARG cc_start: 0.7358 (ptp-170) cc_final: 0.7144 (ptp-110)
REVERT: B  171 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8377 (mm)
REVERT: B  217 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7746 (pmm)
REVERT: G   21 MET cc_start: 0.3769 (tmm) cc_final: 0.3473 (tpt)
  outliers start: 32
  outliers final: 18
  residues processed: 149
  average time/residue: 1.4065
  time to fit residues: 224.7228
Evaluate side-chains
  158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  202 LYS
Chi-restraints excluded: chain R residue  382 ILE
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    0.2980
   chunk 88 optimal weight:    1.9990
   chunk 107 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 1 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN
R 263 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.191875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133064 restraints weight = 10311.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.71
r_work: 0.3286 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9431  Z= 0.175
  Angle     :  0.552   7.677  12787  Z= 0.291
  Chirality :  0.041   0.160   1412
  Planarity :  0.004   0.065   1623
  Dihedral  :  4.903  42.634   1269
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.95 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.25), residues: 1133
  helix:  1.48 (0.26), residues: 438
  sheet:  0.36 (0.33), residues: 234
  loop : -1.63 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 235 
 TYR   0.017   0.001   TYR N  95 
 ARG   0.006   0.000   ARG R  44 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 136
  time to evaluate  : 1.226 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8263 (mt) cc_final: 0.8023 (mp)
REVERT: A  308 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7475 (mt)
REVERT: A  331 ASP cc_start: 0.8016 (t0) cc_final: 0.7728 (t0)
REVERT: A  343 ASP cc_start: 0.7388 (m-30) cc_final: 0.7057 (m-30)
REVERT: A  392 GLU cc_start: 0.7870 (mp0) cc_final: 0.7621 (mm-30)
REVERT: N   34 MET cc_start: 0.8436 (mmm) cc_final: 0.8048 (mmm)
REVERT: N   46 GLU cc_start: 0.8372 (mp0) cc_final: 0.8023 (mp0)
REVERT: N   79 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6943 (tp)
REVERT: P    3 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6790 (mm-30)
REVERT: R   41 GLU cc_start: 0.8441 (pp20) cc_final: 0.7840 (pp20)
REVERT: R  146 ILE cc_start: 0.8737 (mt) cc_final: 0.8456 (mp)
REVERT: R  267 ARG cc_start: 0.7280 (tpt170) cc_final: 0.6230 (mpp80)
REVERT: R  294 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6599 (pp20)
REVERT: R  336 LYS cc_start: 0.7656 (mttp) cc_final: 0.7316 (mmtm)
REVERT: R  348 ARG cc_start: 0.7299 (tpm-80) cc_final: 0.6051 (mtp180)
REVERT: R  376 ARG cc_start: 0.7475 (ptp-170) cc_final: 0.6842 (mtt90)
REVERT: R  387 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5873 (mt-10)
REVERT: R  418 GLU cc_start: 0.6932 (tp30) cc_final: 0.6624 (tm-30)
REVERT: B   42 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7092 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8632 (pt)
REVERT: B  100 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8794 (p)
REVERT: B  134 ARG cc_start: 0.7364 (ptp-170) cc_final: 0.7126 (ptp-110)
REVERT: B  171 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8354 (mm)
REVERT: B  186 ASP cc_start: 0.8318 (m-30) cc_final: 0.7638 (m-30)
REVERT: B  217 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7719 (pmm)
REVERT: G   21 MET cc_start: 0.3820 (tmm) cc_final: 0.3504 (tpt)
  outliers start: 33
  outliers final: 19
  residues processed: 156
  average time/residue: 1.2243
  time to fit residues: 204.8308
Evaluate side-chains
  147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   79 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    3 GLU
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue   72 TRP
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  157 SER
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  382 ILE
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   chunk 100 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  77 ASN
R  45 GLN
B  75 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.188944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.131890 restraints weight = 10137.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.60
r_work: 0.3275 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9431  Z= 0.313
  Angle     :  0.623   7.903  12787  Z= 0.330
  Chirality :  0.044   0.189   1412
  Planarity :  0.004   0.065   1623
  Dihedral  :  5.131  49.472   1269
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.56 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.25), residues: 1133
  helix:  1.26 (0.25), residues: 448
  sheet:  0.25 (0.34), residues: 229
  loop : -1.63 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R  33 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.022   0.002   TYR R 148 
 ARG   0.009   0.000   ARG R  44 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.966 
Fit side-chains
REVERT: A  272 LEU cc_start: 0.8295 (mt) cc_final: 0.8054 (mp)
REVERT: A  283 ARG cc_start: 0.7693 (ptp-110) cc_final: 0.7416 (mtm110)
REVERT: A  308 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7597 (tp)
REVERT: N   34 MET cc_start: 0.8396 (mmm) cc_final: 0.8050 (mmm)
REVERT: N   39 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8047 (tt0)
REVERT: N   46 GLU cc_start: 0.8359 (mp0) cc_final: 0.8034 (mp0)
REVERT: R   41 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7793 (pp20)
REVERT: R   44 ARG cc_start: 0.8594 (ttp80) cc_final: 0.7989 (ptm-80)
REVERT: R  146 ILE cc_start: 0.8787 (mt) cc_final: 0.8500 (mp)
REVERT: R  267 ARG cc_start: 0.7243 (tpt170) cc_final: 0.6218 (mpp80)
REVERT: R  336 LYS cc_start: 0.7681 (mttp) cc_final: 0.7348 (mmtm)
REVERT: R  348 ARG cc_start: 0.7385 (tpm-80) cc_final: 0.6132 (mtp180)
REVERT: R  376 ARG cc_start: 0.7528 (ptp-170) cc_final: 0.6913 (mtt90)
REVERT: R  387 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6037 (mt-10)
REVERT: R  418 GLU cc_start: 0.6990 (tp30) cc_final: 0.6679 (tm-30)
REVERT: B   42 ARG cc_start: 0.7683 (ttp-110) cc_final: 0.7192 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8778 (pt)
REVERT: B  100 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8799 (p)
REVERT: B  134 ARG cc_start: 0.7405 (ptp-170) cc_final: 0.7172 (ptp-110)
REVERT: B  171 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8344 (mm)
REVERT: B  217 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7762 (pmm)
REVERT: G   21 MET cc_start: 0.3639 (tmm) cc_final: 0.3369 (tpt)
  outliers start: 33
  outliers final: 22
  residues processed: 143
  average time/residue: 1.2452
  time to fit residues: 190.2828
Evaluate side-chains
  155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue   41 GLU
Chi-restraints excluded: chain R residue   72 TRP
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  157 SER
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  382 ILE
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.190771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.137796 restraints weight = 10202.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.49
r_work: 0.3304 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9431  Z= 0.266
  Angle     :  0.609   7.726  12787  Z= 0.322
  Chirality :  0.043   0.176   1412
  Planarity :  0.005   0.065   1623
  Dihedral  :  5.152  52.713   1269
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.97 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.25), residues: 1133
  helix:  1.25 (0.25), residues: 449
  sheet:  0.20 (0.34), residues: 230
  loop : -1.61 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP R  33 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.021   0.002   PHE N 108 
 TYR   0.021   0.002   TYR R 148 
 ARG   0.015   0.000   ARG B 197 

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   60 MET cc_start: 0.8217 (mmm) cc_final: 0.7335 (mtt)
REVERT: A  272 LEU cc_start: 0.8343 (mt) cc_final: 0.8140 (mp)
REVERT: A  283 ARG cc_start: 0.7686 (ptp-110) cc_final: 0.7446 (mtm110)
REVERT: A  308 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7680 (tp)
REVERT: A  331 ASP cc_start: 0.8144 (t0) cc_final: 0.7721 (t0)
REVERT: A  386 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8270 (ttm)
REVERT: N   34 MET cc_start: 0.8366 (mmm) cc_final: 0.8050 (mmm)
REVERT: N   39 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8001 (tt0)
REVERT: N   46 GLU cc_start: 0.8396 (mp0) cc_final: 0.8060 (mp0)
REVERT: R   41 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7788 (pp20)
REVERT: R   44 ARG cc_start: 0.8545 (ttp80) cc_final: 0.7925 (ptm-80)
REVERT: R  146 ILE cc_start: 0.8832 (mt) cc_final: 0.8586 (mp)
REVERT: R  267 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6327 (mpp80)
REVERT: R  336 LYS cc_start: 0.7776 (mttp) cc_final: 0.7456 (mmtm)
REVERT: R  348 ARG cc_start: 0.7513 (tpm-80) cc_final: 0.6344 (mtp180)
REVERT: R  376 ARG cc_start: 0.7516 (ptp-170) cc_final: 0.6913 (mtt90)
REVERT: R  387 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6106 (mt-10)
REVERT: R  418 GLU cc_start: 0.7108 (tp30) cc_final: 0.6822 (tm-30)
REVERT: B   42 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7227 (ttm-80)
REVERT: B   70 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8711 (pt)
REVERT: B  100 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8829 (p)
REVERT: B  134 ARG cc_start: 0.7379 (ptp-170) cc_final: 0.7177 (ptp-110)
REVERT: B  171 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8379 (mm)
REVERT: B  217 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7852 (pmm)
REVERT: G   21 MET cc_start: 0.3636 (tmm) cc_final: 0.3388 (tpt)
  outliers start: 31
  outliers final: 21
  residues processed: 149
  average time/residue: 1.1904
  time to fit residues: 189.9360
Evaluate side-chains
  147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  292 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain N residue   39 GLN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   30 VAL
Chi-restraints excluded: chain R residue   41 GLU
Chi-restraints excluded: chain R residue   72 TRP
Chi-restraints excluded: chain R residue  105 THR
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  157 SER
Chi-restraints excluded: chain R residue  174 CYS
Chi-restraints excluded: chain R residue  382 ILE
Chi-restraints excluded: chain R residue  387 GLU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  316 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 68 optimal weight:    0.3980
   chunk 10 optimal weight:    0.0270
   chunk 36 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 43 optimal weight:   50.0000
   chunk 82 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
N  77 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 = 0.4160 r_free = 0.4160 target = 0.192985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.136732 restraints weight = 10142.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.64
r_work: 0.3290 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9431  Z= 0.173
  Angle     :  0.573   7.870  12787  Z= 0.303
  Chirality :  0.041   0.176   1412
  Planarity :  0.004   0.066   1623
  Dihedral  :  5.092  54.037   1269
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.48 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.03 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.25), residues: 1133
  helix:  1.42 (0.25), residues: 449
  sheet:  0.35 (0.33), residues: 234
  loop : -1.56 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP R  33 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 148 
 ARG   0.015   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7064.08 seconds
wall clock time: 124 minutes 10.73 seconds (7450.73 seconds total)