Starting phenix.real_space_refine
on Wed Mar  4 06:12:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5s_33623/03_2026/7y5s_33623.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.040
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    7203      2.51       5
     N    2052      2.21       5
     O    2226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11535
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3845
          Classifications: {'peptide': 505}
          Link IDs: {'PTRANS': 21, 'TRANS': 483}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.60, per 1000 atoms: 0.23
  Number of scatterers: 11535
  At special positions: 0
  Unit cell: (92.2236, 93.3215, 148.217, 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    2226      8.00
     N    2052      7.00
     C    7203      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 528.7 milliseconds
  

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2670

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 18 sheets defined
      4.4% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 68
    Processing helix  chain 'A' and resid 270 through 276
      removed outlier: 3.763A  pdb=" N   ALA A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 68
    Processing helix  chain 'B' and resid 270 through 276
      removed outlier: 3.762A  pdb=" N   ALA B 274 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 68
    Processing helix  chain 'C' and resid 270 through 276
      removed outlier: 3.762A  pdb=" N   ALA C 274 " --> pdb=" O   GLY C 270 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ILE C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   ILE A 124 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   VAL A 182 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER A 151 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ASP A 184 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 153 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL A 224 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS A 186 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL A 226 " --> pdb=" O   HIS A 186 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A 188 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASN A 228 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 9.355A  pdb=" N   ARG A 220 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 10.525A  pdb=" N   ASP A 251 " --> pdb=" O   ARG A 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR A 222 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET A 253 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL A 224 " --> pdb=" O   MET A 253 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   GLN A 255 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL A 226 " --> pdb=" O   GLN A 255 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   SER A 248 " --> pdb=" O   LYS A 292 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   GLU A 294 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR A 250 " --> pdb=" O   GLU A 294 " (cutoff:3.500A)
      removed outlier: 8.094A  pdb=" N   ASN A 296 " --> pdb=" O   THR A 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS A 252 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 252 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   CYS A 254 " --> pdb=" O   PHE A 298 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 139
      removed outlier: 6.799A  pdb=" N   LEU A 173 " --> pdb=" O   PRO A 134 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   PHE A 136 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLN A 175 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA A 138 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE A 194 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   PHE A 196 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLN A 175 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 7.293A  pdb=" N   ASN A 198 " --> pdb=" O   GLN A 175 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP A 232 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLY A 263 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 237 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU A 307 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG A 331 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS A 309 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   ILE A 333 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP A 311 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL A 328 " --> pdb=" O   ASN A 351 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU A 330 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217
      removed outlier: 3.555A  pdb=" N   THR A 216 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS A 245 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ALA A 286 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG A 316 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL A 288 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   CYS A 318 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 8.489A  pdb=" N   GLN A 339 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY A 315 " --> pdb=" O   GLN A 339 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   TYR A 338 " --> pdb=" O   MET A 368 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 394
      removed outlier: 3.772A  pdb=" N   GLY B 416 " --> pdb=" O   ILE B 410 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   GLY A 432 " --> pdb=" O   TRP B 419 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TRP A 429 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN A 448 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU A 431 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   SER B 491 " --> pdb=" O   LEU C 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 492
      removed outlier: 6.306A  pdb=" N   SER A 491 " --> pdb=" O   LEU B 482 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   GLY B 465 " --> pdb=" O   ILE C 456 " (cutoff:3.500A)
      removed outlier: 8.743A  pdb=" N   SER C 458 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   GLN B 467 " --> pdb=" O   SER C 458 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU C 431 " --> pdb=" O   VAL C 446 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   GLN C 448 " --> pdb=" O   TRP C 429 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   TRP C 429 " --> pdb=" O   GLN C 448 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   ALA A 417 " --> pdb=" O   ILE C 430 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   GLY C 432 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   TRP A 419 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   ARG C 434 " --> pdb=" O   TRP A 419 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   ILE A 421 " --> pdb=" O   ARG C 434 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLY A 416 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 391 through 394
      removed outlier: 3.771A  pdb=" N   GLY C 416 " --> pdb=" O   ILE C 410 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY B 432 " --> pdb=" O   TRP C 419 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   TRP B 429 " --> pdb=" O   GLN B 448 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLN B 448 " --> pdb=" O   TRP B 429 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU B 431 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   GLY A 465 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   SER B 458 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   GLN A 467 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 502 through 503
    Processing sheet with id=AA9, first strand: chain 'A' and resid 523 through 524
      removed outlier: 6.963A  pdb=" N   ASN A 523 " --> pdb=" O   ILE B 514 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 74
      removed outlier: 6.062A  pdb=" N   VAL B  73 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   ILE B 124 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 74
      removed outlier: 6.062A  pdb=" N   VAL B  73 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   VAL B 182 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER B 151 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASP B 184 " --> pdb=" O   SER B 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU B 153 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL B 224 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS B 186 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL B 226 " --> pdb=" O   HIS B 186 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY B 188 " --> pdb=" O   VAL B 226 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASN B 228 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 9.356A  pdb=" N   ARG B 220 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 10.526A  pdb=" N   ASP B 251 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR B 222 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET B 253 " --> pdb=" O   THR B 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL B 224 " --> pdb=" O   MET B 253 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLN B 255 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   VAL B 226 " --> pdb=" O   GLN B 255 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   SER B 248 " --> pdb=" O   LYS B 292 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLU B 294 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR B 250 " --> pdb=" O   GLU B 294 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   ASN B 296 " --> pdb=" O   THR B 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS B 252 " --> pdb=" O   ASN B 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE B 298 " --> pdb=" O   CYS B 252 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS B 254 " --> pdb=" O   PHE B 298 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 347 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 139
      removed outlier: 6.799A  pdb=" N   LEU B 173 " --> pdb=" O   PRO B 134 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE B 136 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLN B 175 " --> pdb=" O   PHE B 136 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA B 138 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ILE B 194 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   LEU B 173 " --> pdb=" O   ILE B 194 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   PHE B 196 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   GLN B 175 " --> pdb=" O   PHE B 196 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   ASN B 198 " --> pdb=" O   GLN B 175 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ASP B 232 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY B 263 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL B 237 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   LEU B 307 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ARG B 331 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS B 309 " --> pdb=" O   ARG B 331 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ILE B 333 " --> pdb=" O   HIS B 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP B 311 " --> pdb=" O   ILE B 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL B 328 " --> pdb=" O   ASN B 351 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   VAL B 353 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU B 330 " --> pdb=" O   VAL B 353 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 217
      removed outlier: 3.556A  pdb=" N   THR B 216 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B 245 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ALA B 286 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG B 316 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL B 288 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   CYS B 318 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   GLN B 339 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   GLY B 315 " --> pdb=" O   GLN B 339 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   TYR B 338 " --> pdb=" O   MET B 368 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 523 through 524
      removed outlier: 6.965A  pdb=" N   ASN B 523 " --> pdb=" O   ILE C 514 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL C  73 " --> pdb=" O   PHE C 115 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   ILE C 124 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 72 through 74
      removed outlier: 6.061A  pdb=" N   VAL C  73 " --> pdb=" O   PHE C 115 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   VAL C 182 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   SER C 151 " --> pdb=" O   VAL C 182 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ASP C 184 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU C 153 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL C 224 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   HIS C 186 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL C 226 " --> pdb=" O   HIS C 186 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   GLY C 188 " --> pdb=" O   VAL C 226 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ASN C 228 " --> pdb=" O   GLY C 188 " (cutoff:3.500A)
      removed outlier: 9.354A  pdb=" N   ARG C 220 " --> pdb=" O   PHE C 249 " (cutoff:3.500A)
      removed outlier: 10.524A  pdb=" N   ASP C 251 " --> pdb=" O   ARG C 220 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   THR C 222 " --> pdb=" O   ASP C 251 " (cutoff:3.500A)
      removed outlier: 8.476A  pdb=" N   MET C 253 " --> pdb=" O   THR C 222 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL C 224 " --> pdb=" O   MET C 253 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLN C 255 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   VAL C 226 " --> pdb=" O   GLN C 255 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER C 248 " --> pdb=" O   LYS C 292 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLU C 294 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   THR C 250 " --> pdb=" O   GLU C 294 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   ASN C 296 " --> pdb=" O   THR C 250 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   CYS C 252 " --> pdb=" O   ASN C 296 " (cutoff:3.500A)
      removed outlier: 8.213A  pdb=" N   PHE C 298 " --> pdb=" O   CYS C 252 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   CYS C 254 " --> pdb=" O   PHE C 298 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C 347 " --> pdb=" O   VAL C 324 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 134 through 139
      removed outlier: 6.798A  pdb=" N   LEU C 173 " --> pdb=" O   PRO C 134 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE C 136 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
      removed outlier: 8.164A  pdb=" N   GLN C 175 " --> pdb=" O   PHE C 136 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   ALA C 138 " --> pdb=" O   GLN C 175 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   GLY C 193 " --> pdb=" O   THR C 170 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ASP C 232 " --> pdb=" O   ARG C 192 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   GLY C 263 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL C 237 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU C 307 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ARG C 331 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   HIS C 309 " --> pdb=" O   ARG C 331 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ILE C 333 " --> pdb=" O   HIS C 309 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   ASP C 311 " --> pdb=" O   ILE C 333 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL C 328 " --> pdb=" O   ASN C 351 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   VAL C 353 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   LEU C 330 " --> pdb=" O   VAL C 353 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 216 through 217
      removed outlier: 3.555A  pdb=" N   THR C 216 " --> pdb=" O   SER C 243 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   HIS C 245 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ALA C 286 " --> pdb=" O   GLN C 314 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG C 316 " --> pdb=" O   ALA C 286 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   VAL C 288 " --> pdb=" O   ARG C 316 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   CYS C 318 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   GLN C 339 " --> pdb=" O   ALA C 313 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY C 315 " --> pdb=" O   GLN C 339 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   TYR C 338 " --> pdb=" O   MET C 368 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    648 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: 2.12

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3903
        1.34 -     1.46: 2240
        1.46 -     1.57: 5593
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 11820
  Sorted by residual:
  bond pdb=" CB  PRO B 277 "
       pdb=" CG  PRO B 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.38e+00
  bond pdb=" CB  PRO A 277 "
       pdb=" CG  PRO A 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.34e+00
  bond pdb=" CB  PRO C 277 "
       pdb=" CG  PRO C 277 "
    ideal  model  delta    sigma   weight residual
    1.492  1.568 -0.076 5.00e-02 4.00e+02 2.33e+00
  bond pdb=" CB  ASP C 396 "
       pdb=" CG  ASP C 396 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.26e+00
  bond pdb=" CB  ASP B 396 "
       pdb=" CG  ASP B 396 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.22e+00
  ... (remaining 11815 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 15584
        1.53 -     3.05: 417
        3.05 -     4.58: 79
        4.58 -     6.10: 15
        6.10 -     7.63: 6
  Bond angle restraints: 16101
  Sorted by residual:
  angle pdb=" N   ILE B 521 "
        pdb=" CA  ILE B 521 "
        pdb=" C   ILE B 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.52    4.01 9.80e-01 1.04e+00 1.67e+01
  angle pdb=" N   ILE C 521 "
        pdb=" CA  ILE C 521 "
        pdb=" C   ILE C 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.56    3.97 9.80e-01 1.04e+00 1.64e+01
  angle pdb=" N   ILE A 521 "
        pdb=" CA  ILE A 521 "
        pdb=" C   ILE A 521 "
      ideal   model   delta    sigma   weight residual
     113.53  109.57    3.96 9.80e-01 1.04e+00 1.63e+01
  angle pdb=" C   PHE B 499 "
        pdb=" N   THR B 500 "
        pdb=" CA  THR B 500 "
      ideal   model   delta    sigma   weight residual
     121.54  129.17   -7.63 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   PHE A 499 "
        pdb=" N   THR A 500 "
        pdb=" CA  THR A 500 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  ... (remaining 16096 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.65: 6205
       15.65 -    31.30: 429
       31.30 -    46.95: 119
       46.95 -    62.60: 12
       62.60 -    78.25: 12
  Dihedral angle restraints: 6777
    sinusoidal: 2541
      harmonic: 4236
  Sorted by residual:
  dihedral pdb=" CA  GLU C 156 "
           pdb=" C   GLU C 156 "
           pdb=" N   PRO C 157 "
           pdb=" CA  PRO C 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.85  -21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLU B 156 "
           pdb=" C   GLU B 156 "
           pdb=" N   PRO B 157 "
           pdb=" CA  PRO B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  GLU A 156 "
           pdb=" C   GLU A 156 "
           pdb=" N   PRO A 157 "
           pdb=" CA  PRO A 157 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 6774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1261
       0.050 -    0.099: 343
       0.099 -    0.149: 127
       0.149 -    0.198: 0
       0.198 -    0.248: 3
  Chirality restraints: 1734
  Sorted by residual:
  chirality pdb=" CB  ILE B  70 "
            pdb=" CA  ILE B  70 "
            pdb=" CG1 ILE B  70 "
            pdb=" CG2 ILE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  ILE C  70 "
            pdb=" CA  ILE C  70 "
            pdb=" CG1 ILE C  70 "
            pdb=" CG2 ILE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CB  ILE A  70 "
            pdb=" CA  ILE A  70 "
            pdb=" CG1 ILE A  70 "
            pdb=" CG2 ILE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 1731 not shown)

  Planarity restraints: 2136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 276 "   -0.055 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO B 277 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 277 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 277 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 276 "    0.055 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO C 277 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C 277 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 277 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 276 "   -0.055 5.00e-02 4.00e+02   8.27e-02 1.10e+01
        pdb=" N   PRO A 277 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 2133 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 547
        2.73 -     3.27: 11434
        3.27 -     3.81: 20072
        3.81 -     4.36: 25594
        4.36 -     4.90: 43687
  Nonbonded interactions: 101334
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 278 "
            pdb=" OE1 GLU A 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER C 278 "
            pdb=" OE1 GLU C 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER B 278 "
            pdb=" OE1 GLU B 283 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" O   GLY A 404 "
            pdb=" NH2 ARG C 434 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" NH2 ARG B 434 "
            pdb=" O   GLY C 404 "
     model   vdw
     2.246 3.120
  ... (remaining 101329 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.540
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
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      :  0.003   0.077  11820  Z= 0.127
  Angle     :  0.626   7.630  16101  Z= 0.356
  Chirality :  0.049   0.248   1734
  Planarity :  0.005   0.083   2136
  Dihedral  : 12.391  78.248   4107
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.19), residues: 1509
  helix:  3.94 (0.65), residues: 48
  sheet: -0.28 (0.28), residues: 390
  loop : -2.27 (0.15), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 225 
 TYR   0.014   0.001   TYR A 374 
 PHE   0.011   0.001   PHE C 179 
 TRP   0.016   0.001   TRP C 419 
 HIS   0.002   0.001   HIS C 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11820)
  covalent geometry    : angle       0.62571 (16101)
  hydrogen bonds       : bond        0.17076 (  234)
  hydrogen bonds       : angle       6.65365 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 316
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.6749 (mt) cc_final: 0.6532 (mt)
REVERT: A  289 TYR cc_start: 0.8328 (p90) cc_final: 0.8087 (p90)
REVERT: A  293 HIS cc_start: 0.7395 (m170) cc_final: 0.7056 (m170)
REVERT: B  385 LEU cc_start: 0.8825 (mt) cc_final: 0.8610 (mt)
REVERT: B  470 THR cc_start: 0.8136 (m) cc_final: 0.7822 (p)
REVERT: C   76 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6798 (Cg_exo)
REVERT: C  368 MET cc_start: 0.7761 (mtp) cc_final: 0.7378 (mtm)
REVERT: C  451 TYR cc_start: 0.7854 (t80) cc_final: 0.7623 (t80)
REVERT: C  470 THR cc_start: 0.8211 (m) cc_final: 0.7873 (p)
REVERT: C  519 ASP cc_start: 0.6226 (t0) cc_final: 0.5852 (t0)
  outliers start: 0
  outliers final: 2
  residues processed: 316
  average time/residue: 0.3471
  time to fit residues: 123.9581
Evaluate side-chains
  249 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 247
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain C residue  357 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.0050
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    2.1400

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 110 GLN
A 242 ASN
A 247 ASN
A 255 GLN
A 291 ASN
A 376 GLN
A 436 GLN
B  69 ASN
B  89 ASN
B 242 ASN
B 290 ASN
B 402 ASN
B 436 GLN
C  89 ASN
C 110 GLN
C 242 ASN
C 255 GLN
C 290 ASN
C 376 GLN
C 402 ASN
** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.145285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.131399 restraints weight = 15889.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.09
r_work: 0.3633 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  11820  Z= 0.295
  Angle     :  0.763  12.631  16101  Z= 0.418
  Chirality :  0.056   0.250   1734
  Planarity :  0.006   0.055   2136
  Dihedral  :  6.699  78.016   1654
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 11.80 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.19), residues: 1509
  helix:  4.02 (0.69), residues: 48
  sheet: -0.48 (0.26), residues: 426
  loop : -2.29 (0.16), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 440 
 TYR   0.016   0.002   TYR B 374 
 PHE   0.030   0.003   PHE B 474 
 TRP   0.039   0.003   TRP B 419 
 HIS   0.010   0.002   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (11820)
  covalent geometry    : angle       0.76285 (16101)
  hydrogen bonds       : bond        0.04615 (  234)
  hydrogen bonds       : angle       6.52657 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 278
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  142 TRP cc_start: 0.6943 (p90) cc_final: 0.6708 (p90)
REVERT: A  212 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7833 (ptmt)
REVERT: A  233 VAL cc_start: 0.6650 (p) cc_final: 0.6390 (m)
REVERT: A  264 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6629 (ttm)
REVERT: A  291 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (m-40)
REVERT: A  293 HIS cc_start: 0.8143 (m170) cc_final: 0.7799 (m-70)
REVERT: A  301 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8218 (m-30)
REVERT: A  400 SER cc_start: 0.8226 (m) cc_final: 0.7971 (m)
REVERT: A  470 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8275 (p)
REVERT: A  518 GLN cc_start: 0.8294 (mt0) cc_final: 0.8057 (mt0)
REVERT: B  110 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7236 (mt0)
REVERT: B  145 HIS cc_start: 0.7804 (p-80) cc_final: 0.7486 (p90)
REVERT: B  158 VAL cc_start: 0.7825 (t) cc_final: 0.7519 (t)
REVERT: B  230 ASP cc_start: 0.7965 (m-30) cc_final: 0.7471 (m-30)
REVERT: B  266 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7853 (mtp)
REVERT: B  293 HIS cc_start: 0.8270 (m170) cc_final: 0.7827 (m-70)
REVERT: B  385 LEU cc_start: 0.9027 (mt) cc_final: 0.8718 (mp)
REVERT: B  388 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8429 (m)
REVERT: B  396 ASP cc_start: 0.7480 (t70) cc_final: 0.7141 (t0)
REVERT: C  102 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6749 (mpt-90)
REVERT: C  160 TRP cc_start: 0.7800 (t60) cc_final: 0.7176 (t-100)
REVERT: C  258 SER cc_start: 0.7238 (OUTLIER) cc_final: 0.6958 (p)
REVERT: C  266 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8077 (ptp)
REVERT: C  276 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7783 (ttp-110)
REVERT: C  308 MET cc_start: 0.8189 (ttm) cc_final: 0.7975 (ttm)
REVERT: C  357 ASP cc_start: 0.8182 (t70) cc_final: 0.7964 (OUTLIER)
REVERT: C  368 MET cc_start: 0.8471 (mtp) cc_final: 0.8199 (mtp)
REVERT: C  385 LEU cc_start: 0.9019 (mt) cc_final: 0.8714 (mt)
REVERT: C  396 ASP cc_start: 0.7519 (t0) cc_final: 0.7299 (t0)
REVERT: C  470 THR cc_start: 0.8440 (m) cc_final: 0.8215 (p)
REVERT: C  518 GLN cc_start: 0.8328 (mt0) cc_final: 0.8056 (mt0)
  outliers start: 48
  outliers final: 19
  residues processed: 298
  average time/residue: 0.3738
  time to fit residues: 124.7038
Evaluate side-chains
  271 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 242
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  291 ASN
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  335 GLN
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  396 ASP
Chi-restraints excluded: chain A residue  418 ILE
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  266 MET
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  266 MET
Chi-restraints excluded: chain C residue  354 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  418 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
A 414 ASN
B  89 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
C  56 GLN
C 145 HIS
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.146493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.132556 restraints weight = 16137.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3742 rms_B_bonded: 2.15
r_work: 0.3651 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11820  Z= 0.168
  Angle     :  0.655   8.350  16101  Z= 0.352
  Chirality :  0.052   0.207   1734
  Planarity :  0.005   0.048   2136
  Dihedral  :  5.960  24.654   1650
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.74 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.20), residues: 1509
  helix:  3.91 (0.67), residues: 48
  sheet: -0.63 (0.27), residues: 390
  loop : -2.16 (0.16), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 440 
 TYR   0.021   0.002   TYR A 395 
 PHE   0.019   0.002   PHE C 115 
 TRP   0.029   0.002   TRP B 419 
 HIS   0.005   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (11820)
  covalent geometry    : angle       0.65469 (16101)
  hydrogen bonds       : bond        0.03557 (  234)
  hydrogen bonds       : angle       5.96051 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 250
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6696 (tpt) cc_final: 0.5992 (tpt)
REVERT: A  115 PHE cc_start: 0.8363 (p90) cc_final: 0.8042 (p90)
REVERT: A  145 HIS cc_start: 0.8008 (p-80) cc_final: 0.7695 (p-80)
REVERT: A  233 VAL cc_start: 0.6639 (p) cc_final: 0.6416 (m)
REVERT: A  262 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7509 (mm)
REVERT: A  301 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8208 (m-30)
REVERT: A  400 SER cc_start: 0.8325 (m) cc_final: 0.8018 (m)
REVERT: A  470 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8204 (p)
REVERT: A  518 GLN cc_start: 0.8313 (mt0) cc_final: 0.8090 (mt0)
REVERT: B   38 PHE cc_start: 0.6650 (m-80) cc_final: 0.6355 (m-80)
REVERT: B   41 VAL cc_start: 0.8133 (p) cc_final: 0.7894 (m)
REVERT: B   83 MET cc_start: 0.6692 (tpp) cc_final: 0.6478 (tpt)
REVERT: B  110 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7266 (mt0)
REVERT: B  158 VAL cc_start: 0.7847 (t) cc_final: 0.7566 (t)
REVERT: B  230 ASP cc_start: 0.7883 (m-30) cc_final: 0.7505 (m-30)
REVERT: B  293 HIS cc_start: 0.8149 (m170) cc_final: 0.7695 (m-70)
REVERT: B  298 PHE cc_start: 0.7968 (t80) cc_final: 0.7747 (t80)
REVERT: B  347 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7598 (pp)
REVERT: B  385 LEU cc_start: 0.8943 (mt) cc_final: 0.8716 (mp)
REVERT: B  388 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8449 (m)
REVERT: B  396 ASP cc_start: 0.7297 (t70) cc_final: 0.6943 (t0)
REVERT: B  481 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7197 (tp)
REVERT: C  102 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6706 (mpt-90)
REVERT: C  160 TRP cc_start: 0.7828 (t60) cc_final: 0.7089 (t-100)
REVERT: C  212 LYS cc_start: 0.8669 (pttt) cc_final: 0.8394 (ptpp)
REVERT: C  357 ASP cc_start: 0.8157 (t70) cc_final: 0.7946 (OUTLIER)
REVERT: C  368 MET cc_start: 0.8366 (mtp) cc_final: 0.8158 (mtp)
REVERT: C  385 LEU cc_start: 0.8931 (mt) cc_final: 0.8554 (mp)
REVERT: C  396 ASP cc_start: 0.7522 (t0) cc_final: 0.7224 (t0)
REVERT: C  409 ASN cc_start: 0.7696 (m-40) cc_final: 0.7470 (m110)
REVERT: C  410 ILE cc_start: 0.8524 (mt) cc_final: 0.8313 (mt)
REVERT: C  470 THR cc_start: 0.8510 (m) cc_final: 0.8274 (p)
REVERT: C  518 GLN cc_start: 0.8294 (mt0) cc_final: 0.7998 (mt0)
  outliers start: 35
  outliers final: 15
  residues processed: 269
  average time/residue: 0.3966
  time to fit residues: 119.0610
Evaluate side-chains
  255 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 233
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  481 LEU
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 131 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  60 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 290 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
A 463 ASN
B 198 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 159 ASN
C 164 ASN
C 219 ASN
C 376 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.139562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.126197 restraints weight = 16066.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.09
r_work: 0.3566 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.5411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  11820  Z= 0.285
  Angle     :  0.751  14.463  16101  Z= 0.403
  Chirality :  0.056   0.266   1734
  Planarity :  0.006   0.048   2136
  Dihedral  :  6.467  27.362   1650
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 17.41 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.19), residues: 1509
  helix:  3.63 (0.68), residues: 48
  sheet: -0.79 (0.26), residues: 396
  loop : -2.36 (0.16), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 225 
 TYR   0.022   0.002   TYR C 235 
 PHE   0.035   0.003   PHE B 474 
 TRP   0.037   0.003   TRP B 419 
 HIS   0.007   0.003   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 (11820)
  covalent geometry    : angle       0.75118 (16101)
  hydrogen bonds       : bond        0.04446 (  234)
  hydrogen bonds       : angle       6.46714 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 239
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  115 PHE cc_start: 0.8403 (p90) cc_final: 0.8050 (p90)
REVERT: A  212 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7797 (ptmt)
REVERT: A  233 VAL cc_start: 0.6662 (p) cc_final: 0.6411 (m)
REVERT: A  262 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7643 (mm)
REVERT: A  301 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (m-30)
REVERT: A  400 SER cc_start: 0.8251 (m) cc_final: 0.7939 (m)
REVERT: A  463 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7277 (p0)
REVERT: A  526 SER cc_start: 0.7302 (t) cc_final: 0.6997 (p)
REVERT: B   41 VAL cc_start: 0.8327 (p) cc_final: 0.8116 (m)
REVERT: B   52 THR cc_start: 0.7511 (p) cc_final: 0.7166 (p)
REVERT: B   83 MET cc_start: 0.6897 (tpp) cc_final: 0.6571 (tpt)
REVERT: B  110 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7265 (mt0)
REVERT: B  208 ASN cc_start: 0.8066 (m-40) cc_final: 0.7788 (m-40)
REVERT: B  230 ASP cc_start: 0.7968 (m-30) cc_final: 0.7555 (m-30)
REVERT: B  231 ILE cc_start: 0.6732 (mm) cc_final: 0.6505 (mm)
REVERT: B  255 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7384 (tm-30)
REVERT: B  289 TYR cc_start: 0.8257 (p90) cc_final: 0.8025 (p90)
REVERT: B  293 HIS cc_start: 0.8289 (m170) cc_final: 0.7811 (m-70)
REVERT: B  347 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7624 (pp)
REVERT: B  385 LEU cc_start: 0.8932 (mt) cc_final: 0.8696 (mp)
REVERT: B  388 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8527 (m)
REVERT: B  396 ASP cc_start: 0.7456 (t70) cc_final: 0.7108 (OUTLIER)
REVERT: B  447 TRP cc_start: 0.8325 (m100) cc_final: 0.8047 (m100)
REVERT: C   43 ASP cc_start: 0.7505 (p0) cc_final: 0.7274 (p0)
REVERT: C   83 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6521 (tpt)
REVERT: C  102 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6512 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7869 (p-80) cc_final: 0.7048 (p-80)
REVERT: C  160 TRP cc_start: 0.7977 (t60) cc_final: 0.7295 (t-100)
REVERT: C  357 ASP cc_start: 0.8062 (t70) cc_final: 0.7850 (t0)
REVERT: C  368 MET cc_start: 0.8384 (mtp) cc_final: 0.8152 (mtp)
REVERT: C  385 LEU cc_start: 0.8969 (mt) cc_final: 0.8622 (mp)
REVERT: C  388 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8543 (m)
REVERT: C  396 ASP cc_start: 0.7569 (t0) cc_final: 0.7238 (t0)
REVERT: C  409 ASN cc_start: 0.7639 (m-40) cc_final: 0.7387 (m110)
REVERT: C  455 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8432 (t)
REVERT: C  483 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6849 (ptt-90)
REVERT: C  518 GLN cc_start: 0.8374 (mt0) cc_final: 0.8121 (mt0)
  outliers start: 63
  outliers final: 26
  residues processed: 278
  average time/residue: 0.3898
  time to fit residues: 121.0403
Evaluate side-chains
  261 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 223
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  322 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  396 ASP
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  215 PHE
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  354 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  388 SER
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  439 SER
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  483 ARG
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0970
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 376 GLN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
C 159 ASN
C 164 ASN
C 376 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.131428 restraints weight = 15952.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 2.12
r_work: 0.3635 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11820  Z= 0.131
  Angle     :  0.632  11.304  16101  Z= 0.335
  Chirality :  0.050   0.200   1734
  Planarity :  0.005   0.047   2136
  Dihedral  :  5.967  25.437   1650
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 20.21 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.20), residues: 1509
  helix:  3.65 (0.66), residues: 48
  sheet: -0.63 (0.27), residues: 366
  loop : -2.26 (0.16), residues: 1095

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 530 
 TYR   0.016   0.001   TYR B 395 
 PHE   0.024   0.001   PHE B 474 
 TRP   0.020   0.002   TRP C 419 
 HIS   0.007   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11820)
  covalent geometry    : angle       0.63168 (16101)
  hydrogen bonds       : bond        0.03009 (  234)
  hydrogen bonds       : angle       5.86502 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 242
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7488 (p) cc_final: 0.7116 (p)
REVERT: A  115 PHE cc_start: 0.8331 (p90) cc_final: 0.7944 (p90)
REVERT: A  156 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5553 (tp30)
REVERT: A  262 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7801 (mp)
REVERT: A  301 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (m-30)
REVERT: A  396 ASP cc_start: 0.7681 (t70) cc_final: 0.7418 (t0)
REVERT: A  526 SER cc_start: 0.7272 (t) cc_final: 0.6974 (p)
REVERT: B   41 VAL cc_start: 0.8334 (p) cc_final: 0.8132 (m)
REVERT: B   83 MET cc_start: 0.6752 (tpp) cc_final: 0.6490 (tpt)
REVERT: B  139 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5835 (mtt-85)
REVERT: B  208 ASN cc_start: 0.8042 (m-40) cc_final: 0.7733 (m110)
REVERT: B  230 ASP cc_start: 0.7872 (m-30) cc_final: 0.7513 (m-30)
REVERT: B  255 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7248 (tm-30)
REVERT: B  293 HIS cc_start: 0.8160 (m170) cc_final: 0.7680 (m-70)
REVERT: B  383 ASP cc_start: 0.7490 (t0) cc_final: 0.7074 (p0)
REVERT: B  388 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8534 (m)
REVERT: B  396 ASP cc_start: 0.7156 (t70) cc_final: 0.6859 (t0)
REVERT: B  447 TRP cc_start: 0.8281 (m100) cc_final: 0.8008 (m100)
REVERT: B  480 THR cc_start: 0.8212 (m) cc_final: 0.7910 (t)
REVERT: C  102 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6528 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7880 (p-80) cc_final: 0.7141 (p-80)
REVERT: C  156 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5060 (tt0)
REVERT: C  160 TRP cc_start: 0.7902 (t60) cc_final: 0.7186 (t-100)
REVERT: C  212 LYS cc_start: 0.8551 (pttt) cc_final: 0.8239 (ptpp)
REVERT: C  357 ASP cc_start: 0.8034 (t70) cc_final: 0.7834 (t0)
REVERT: C  368 MET cc_start: 0.8311 (mtp) cc_final: 0.8107 (mtp)
REVERT: C  385 LEU cc_start: 0.8919 (mt) cc_final: 0.8613 (mp)
REVERT: C  396 ASP cc_start: 0.7404 (t0) cc_final: 0.7071 (t0)
REVERT: C  470 THR cc_start: 0.8552 (m) cc_final: 0.8248 (p)
REVERT: C  518 GLN cc_start: 0.8324 (mt0) cc_final: 0.8034 (mt0)
  outliers start: 48
  outliers final: 18
  residues processed: 271
  average time/residue: 0.4373
  time to fit residues: 131.5569
Evaluate side-chains
  251 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 225
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 140 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   chunk 114 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 148 optimal weight:    0.5980
   chunk 107 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 219 ASN
C 291 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.139333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.125904 restraints weight = 16079.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.12
r_work: 0.3590 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3437 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11820  Z= 0.206
  Angle     :  0.682  13.318  16101  Z= 0.360
  Chirality :  0.052   0.211   1734
  Planarity :  0.005   0.046   2136
  Dihedral  :  6.142  25.599   1650
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 21.12 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.33 (0.20), residues: 1509
  helix:  3.61 (0.67), residues: 48
  sheet: -0.77 (0.26), residues: 378
  loop : -2.26 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 530 
 TYR   0.021   0.002   TYR C 235 
 PHE   0.020   0.002   PHE B 474 
 TRP   0.030   0.002   TRP B 419 
 HIS   0.005   0.002   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (11820)
  covalent geometry    : angle       0.68152 (16101)
  hydrogen bonds       : bond        0.03552 (  234)
  hydrogen bonds       : angle       6.12672 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 246
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7643 (p) cc_final: 0.7286 (p)
REVERT: A   83 MET cc_start: 0.6722 (tpt) cc_final: 0.6414 (tmm)
REVERT: A  115 PHE cc_start: 0.8348 (p90) cc_final: 0.7977 (p90)
REVERT: A  174 LEU cc_start: 0.8380 (mt) cc_final: 0.8140 (mt)
REVERT: A  212 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7816 (ptmt)
REVERT: A  262 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (mp)
REVERT: A  301 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8285 (m-30)
REVERT: A  396 ASP cc_start: 0.7548 (t70) cc_final: 0.7209 (t0)
REVERT: A  526 SER cc_start: 0.7368 (t) cc_final: 0.7020 (p)
REVERT: B   41 VAL cc_start: 0.8375 (p) cc_final: 0.8173 (m)
REVERT: B   83 MET cc_start: 0.6833 (tpp) cc_final: 0.6633 (tpt)
REVERT: B  139 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.5826 (mtt-85)
REVERT: B  156 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5477 (tt0)
REVERT: B  175 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7437 (pp30)
REVERT: B  208 ASN cc_start: 0.8043 (m-40) cc_final: 0.7775 (m110)
REVERT: B  230 ASP cc_start: 0.7937 (m-30) cc_final: 0.7543 (m-30)
REVERT: B  235 TYR cc_start: 0.7902 (m-80) cc_final: 0.7621 (m-80)
REVERT: B  255 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7149 (tm-30)
REVERT: B  279 SER cc_start: 0.8361 (m) cc_final: 0.8156 (p)
REVERT: B  289 TYR cc_start: 0.8226 (p90) cc_final: 0.7971 (p90)
REVERT: B  383 ASP cc_start: 0.7625 (t0) cc_final: 0.7185 (p0)
REVERT: B  388 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8530 (m)
REVERT: B  396 ASP cc_start: 0.7363 (t70) cc_final: 0.7031 (t0)
REVERT: B  447 TRP cc_start: 0.8294 (m100) cc_final: 0.8044 (m100)
REVERT: C  102 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6520 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7917 (p-80) cc_final: 0.7170 (p-80)
REVERT: C  156 GLU cc_start: 0.5675 (OUTLIER) cc_final: 0.5226 (tt0)
REVERT: C  258 SER cc_start: 0.7254 (m) cc_final: 0.6958 (p)
REVERT: C  385 LEU cc_start: 0.8890 (mt) cc_final: 0.8597 (mp)
REVERT: C  396 ASP cc_start: 0.7450 (t0) cc_final: 0.7045 (t0)
REVERT: C  518 GLN cc_start: 0.8342 (mt0) cc_final: 0.8042 (mt0)
  outliers start: 55
  outliers final: 23
  residues processed: 280
  average time/residue: 0.4521
  time to fit residues: 139.8926
Evaluate side-chains
  268 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 235
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  258 SER
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 137 optimal weight:    0.7980
   chunk 132 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   chunk 36 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 147 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 HIS
A 399 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
B 463 ASN
C 219 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.142000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.128533 restraints weight = 16194.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.16
r_work: 0.3630 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.5616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11820  Z= 0.131
  Angle     :  0.630  11.868  16101  Z= 0.332
  Chirality :  0.050   0.183   1734
  Planarity :  0.005   0.045   2136
  Dihedral  :  5.879  23.757   1650
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 22.52 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.20), residues: 1509
  helix:  3.65 (0.66), residues: 48
  sheet: -0.70 (0.27), residues: 378
  loop : -2.21 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 530 
 TYR   0.014   0.001   TYR B 395 
 PHE   0.021   0.001   PHE A 215 
 TRP   0.022   0.001   TRP B 419 
 HIS   0.004   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (11820)
  covalent geometry    : angle       0.62971 (16101)
  hydrogen bonds       : bond        0.02845 (  234)
  hydrogen bonds       : angle       5.89555 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7693 (p) cc_final: 0.7340 (p)
REVERT: A   83 MET cc_start: 0.6732 (tpt) cc_final: 0.6454 (tmm)
REVERT: A  115 PHE cc_start: 0.8360 (p90) cc_final: 0.8030 (p90)
REVERT: A  212 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7902 (ptmt)
REVERT: A  262 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (mp)
REVERT: A  276 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7795 (ttm170)
REVERT: A  396 ASP cc_start: 0.7547 (t70) cc_final: 0.7235 (t0)
REVERT: A  400 SER cc_start: 0.8346 (p) cc_final: 0.7844 (m)
REVERT: A  526 SER cc_start: 0.7347 (t) cc_final: 0.6975 (p)
REVERT: B  139 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.5762 (mtt-85)
REVERT: B  208 ASN cc_start: 0.8030 (m-40) cc_final: 0.7763 (m110)
REVERT: B  217 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7678 (mt-10)
REVERT: B  230 ASP cc_start: 0.7908 (m-30) cc_final: 0.7560 (m-30)
REVERT: B  235 TYR cc_start: 0.7919 (m-80) cc_final: 0.7610 (m-80)
REVERT: B  255 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7180 (tm-30)
REVERT: B  279 SER cc_start: 0.8301 (m) cc_final: 0.8084 (p)
REVERT: B  289 TYR cc_start: 0.8182 (p90) cc_final: 0.7951 (p90)
REVERT: B  388 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8501 (m)
REVERT: B  396 ASP cc_start: 0.7177 (t70) cc_final: 0.6860 (t0)
REVERT: B  434 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8223 (ptt90)
REVERT: B  447 TRP cc_start: 0.8290 (m100) cc_final: 0.7959 (m100)
REVERT: C  102 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6562 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7883 (p-80) cc_final: 0.7186 (p-80)
REVERT: C  156 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5176 (tt0)
REVERT: C  212 LYS cc_start: 0.8468 (pttt) cc_final: 0.8189 (ptpp)
REVERT: C  385 LEU cc_start: 0.8938 (mt) cc_final: 0.8681 (mp)
REVERT: C  396 ASP cc_start: 0.7338 (t0) cc_final: 0.6973 (t0)
REVERT: C  470 THR cc_start: 0.8623 (m) cc_final: 0.8296 (p)
  outliers start: 45
  outliers final: 19
  residues processed: 265
  average time/residue: 0.4420
  time to fit residues: 129.2519
Evaluate side-chains
  262 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 235
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 99 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.127368 restraints weight = 16216.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.11
r_work: 0.3622 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.5653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11820  Z= 0.141
  Angle     :  0.633  12.574  16101  Z= 0.333
  Chirality :  0.050   0.176   1734
  Planarity :  0.005   0.044   2136
  Dihedral  :  5.813  22.463   1650
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 22.52 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.20), residues: 1509
  helix:  3.67 (0.66), residues: 48
  sheet: -0.57 (0.27), residues: 387
  loop : -2.23 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 316 
 TYR   0.014   0.001   TYR C 284 
 PHE   0.024   0.001   PHE B 215 
 TRP   0.023   0.001   TRP B 419 
 HIS   0.004   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11820)
  covalent geometry    : angle       0.63282 (16101)
  hydrogen bonds       : bond        0.02968 (  234)
  hydrogen bonds       : angle       5.86063 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 241
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7749 (p) cc_final: 0.7413 (p)
REVERT: A   83 MET cc_start: 0.6720 (tpt) cc_final: 0.6464 (tmm)
REVERT: A  115 PHE cc_start: 0.8366 (p90) cc_final: 0.8031 (p90)
REVERT: A  212 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7916 (ptmt)
REVERT: A  262 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7737 (mp)
REVERT: A  276 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7822 (ttm170)
REVERT: A  301 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8295 (m-30)
REVERT: A  396 ASP cc_start: 0.7575 (t70) cc_final: 0.7219 (t0)
REVERT: A  400 SER cc_start: 0.8353 (p) cc_final: 0.7870 (m)
REVERT: A  526 SER cc_start: 0.7341 (t) cc_final: 0.6968 (p)
REVERT: B   41 VAL cc_start: 0.8366 (m) cc_final: 0.8084 (p)
REVERT: B  139 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.5803 (mtt-85)
REVERT: B  175 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7204 (pt0)
REVERT: B  208 ASN cc_start: 0.8016 (m-40) cc_final: 0.7749 (m110)
REVERT: B  217 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7744 (mt-10)
REVERT: B  230 ASP cc_start: 0.7862 (m-30) cc_final: 0.7533 (m-30)
REVERT: B  235 TYR cc_start: 0.7924 (m-80) cc_final: 0.7608 (m-80)
REVERT: B  255 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7450 (tm-30)
REVERT: B  279 SER cc_start: 0.8318 (m) cc_final: 0.8104 (p)
REVERT: B  289 TYR cc_start: 0.8220 (p90) cc_final: 0.7981 (p90)
REVERT: B  383 ASP cc_start: 0.7591 (t0) cc_final: 0.7230 (p0)
REVERT: B  388 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8427 (m)
REVERT: B  396 ASP cc_start: 0.7109 (t70) cc_final: 0.6817 (t0)
REVERT: B  434 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.6513 (ptp90)
REVERT: B  447 TRP cc_start: 0.8258 (m100) cc_final: 0.7991 (m100)
REVERT: C  102 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6560 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7861 (p-80) cc_final: 0.7158 (p-80)
REVERT: C  156 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5134 (tt0)
REVERT: C  212 LYS cc_start: 0.8515 (pttt) cc_final: 0.8227 (ptpp)
REVERT: C  258 SER cc_start: 0.7245 (OUTLIER) cc_final: 0.6957 (p)
REVERT: C  264 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6262 (tmt)
REVERT: C  266 MET cc_start: 0.7938 (ptp) cc_final: 0.7737 (ptp)
REVERT: C  385 LEU cc_start: 0.8937 (mt) cc_final: 0.8682 (mp)
REVERT: C  396 ASP cc_start: 0.7323 (t0) cc_final: 0.6907 (t0)
  outliers start: 51
  outliers final: 22
  residues processed: 269
  average time/residue: 0.4408
  time to fit residues: 131.3647
Evaluate side-chains
  267 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 233
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  264 MET
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 148 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 126 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
C 376 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.141259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.128037 restraints weight = 16059.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.11
r_work: 0.3642 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.5704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11820  Z= 0.133
  Angle     :  0.626  11.434  16101  Z= 0.330
  Chirality :  0.050   0.176   1734
  Planarity :  0.005   0.044   2136
  Dihedral  :  5.760  21.820   1650
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 23.76 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.20), residues: 1509
  helix:  3.63 (0.67), residues: 48
  sheet: -0.58 (0.27), residues: 387
  loop : -2.22 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 530 
 TYR   0.014   0.001   TYR C 120 
 PHE   0.025   0.001   PHE B 215 
 TRP   0.021   0.001   TRP B 419 
 HIS   0.006   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11820)
  covalent geometry    : angle       0.62608 (16101)
  hydrogen bonds       : bond        0.02830 (  234)
  hydrogen bonds       : angle       5.86475 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 238
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7757 (p) cc_final: 0.7441 (p)
REVERT: A   83 MET cc_start: 0.6692 (tpt) cc_final: 0.6416 (tmm)
REVERT: A  115 PHE cc_start: 0.8361 (p90) cc_final: 0.8002 (p90)
REVERT: A  212 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7934 (ptmt)
REVERT: A  262 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7702 (mp)
REVERT: A  396 ASP cc_start: 0.7556 (t70) cc_final: 0.7202 (t0)
REVERT: A  400 SER cc_start: 0.8376 (p) cc_final: 0.7876 (m)
REVERT: A  526 SER cc_start: 0.7366 (t) cc_final: 0.6986 (p)
REVERT: B   41 VAL cc_start: 0.8380 (m) cc_final: 0.8090 (p)
REVERT: B  139 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.5818 (mtt-85)
REVERT: B  175 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7150 (pt0)
REVERT: B  208 ASN cc_start: 0.7989 (m-40) cc_final: 0.7747 (m110)
REVERT: B  217 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7696 (mt-10)
REVERT: B  230 ASP cc_start: 0.7813 (m-30) cc_final: 0.7492 (m-30)
REVERT: B  235 TYR cc_start: 0.7834 (m-80) cc_final: 0.7450 (m-80)
REVERT: B  255 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7414 (tm-30)
REVERT: B  279 SER cc_start: 0.8316 (m) cc_final: 0.8102 (p)
REVERT: B  383 ASP cc_start: 0.7584 (t0) cc_final: 0.7182 (p0)
REVERT: B  388 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8412 (m)
REVERT: B  396 ASP cc_start: 0.7000 (t70) cc_final: 0.6782 (OUTLIER)
REVERT: B  434 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8211 (ptt90)
REVERT: B  447 TRP cc_start: 0.8228 (m100) cc_final: 0.7956 (m100)
REVERT: C  102 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6571 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7841 (p-80) cc_final: 0.7139 (p-80)
REVERT: C  156 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5126 (tt0)
REVERT: C  212 LYS cc_start: 0.8518 (pttt) cc_final: 0.8236 (ptpp)
REVERT: C  258 SER cc_start: 0.7262 (OUTLIER) cc_final: 0.6974 (p)
REVERT: C  385 LEU cc_start: 0.8916 (mt) cc_final: 0.8668 (mp)
REVERT: C  396 ASP cc_start: 0.7285 (t0) cc_final: 0.6842 (t0)
  outliers start: 39
  outliers final: 23
  residues processed: 262
  average time/residue: 0.4377
  time to fit residues: 127.1852
Evaluate side-chains
  266 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 234
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  439 SER
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 138 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 28 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 255 GLN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 ASN
C 219 ASN
C 376 GLN
C 463 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.136468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123400 restraints weight = 16278.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.07
r_work: 0.3571 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11820  Z= 0.231
  Angle     :  0.703  11.451  16101  Z= 0.373
  Chirality :  0.053   0.221   1734
  Planarity :  0.006   0.066   2136
  Dihedral  :  6.167  25.296   1650
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 23.76 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.20), residues: 1509
  helix:  3.55 (0.68), residues: 48
  sheet: -0.74 (0.27), residues: 387
  loop : -2.30 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 444 
 TYR   0.023   0.002   TYR C 235 
 PHE   0.017   0.002   PHE C 196 
 TRP   0.029   0.002   TRP B 419 
 HIS   0.008   0.002   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (11820)
  covalent geometry    : angle       0.70337 (16101)
  hydrogen bonds       : bond        0.03659 (  234)
  hydrogen bonds       : angle       6.25282 (  648)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 246
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7805 (p) cc_final: 0.7483 (p)
REVERT: A   83 MET cc_start: 0.6767 (tpt) cc_final: 0.6521 (tmm)
REVERT: A  115 PHE cc_start: 0.8394 (p90) cc_final: 0.8017 (p90)
REVERT: A  212 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7916 (ptmt)
REVERT: A  255 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7714 (tp40)
REVERT: A  262 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7802 (mp)
REVERT: A  396 ASP cc_start: 0.7640 (t70) cc_final: 0.7251 (t0)
REVERT: A  400 SER cc_start: 0.8376 (p) cc_final: 0.7876 (m)
REVERT: A  526 SER cc_start: 0.7533 (t) cc_final: 0.7109 (p)
REVERT: B   41 VAL cc_start: 0.8431 (m) cc_final: 0.8125 (p)
REVERT: B  139 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.5856 (mtt-85)
REVERT: B  175 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7325 (pp30)
REVERT: B  208 ASN cc_start: 0.8024 (m-40) cc_final: 0.7759 (m110)
REVERT: B  230 ASP cc_start: 0.7920 (m-30) cc_final: 0.7551 (m-30)
REVERT: B  235 TYR cc_start: 0.7955 (m-80) cc_final: 0.7589 (m-80)
REVERT: B  255 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7571 (tm-30)
REVERT: B  388 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8504 (m)
REVERT: B  396 ASP cc_start: 0.7134 (t70) cc_final: 0.6895 (OUTLIER)
REVERT: B  434 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.6769 (ptp90)
REVERT: B  447 TRP cc_start: 0.8280 (m100) cc_final: 0.8007 (m100)
REVERT: C  102 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6557 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7803 (p-80) cc_final: 0.7118 (p-80)
REVERT: C  156 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5139 (tt0)
REVERT: C  258 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.7077 (p)
REVERT: C  385 LEU cc_start: 0.8902 (mt) cc_final: 0.8671 (mp)
REVERT: C  396 ASP cc_start: 0.7424 (t0) cc_final: 0.7014 (t0)
  outliers start: 41
  outliers final: 22
  residues processed: 274
  average time/residue: 0.4307
  time to fit residues: 130.9081
Evaluate side-chains
  268 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  463 ASN
Chi-restraints excluded: chain A residue  491 SER
Chi-restraints excluded: chain B residue  109 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  139 ARG
Chi-restraints excluded: chain B residue  175 GLN
Chi-restraints excluded: chain B residue  255 GLN
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  439 SER
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  463 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 123 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 135 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.123515 restraints weight = 16293.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 2.08
r_work: 0.3573 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3422 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.5902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.140  11820  Z= 0.263
  Angle     :  1.108  59.200  16101  Z= 0.662
  Chirality :  0.059   0.907   1734
  Planarity :  0.006   0.061   2136
  Dihedral  :  6.155  25.224   1650
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.59 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.20), residues: 1509
  helix:  3.56 (0.68), residues: 48
  sheet: -0.75 (0.27), residues: 387
  loop : -2.30 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 440 
 TYR   0.021   0.002   TYR C 235 
 PHE   0.019   0.002   PHE B 215 
 TRP   0.028   0.002   TRP B 419 
 HIS   0.006   0.002   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 (11820)
  covalent geometry    : angle       1.10799 (16101)
  hydrogen bonds       : bond        0.03617 (  234)
  hydrogen bonds       : angle       6.25128 (  648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3810.99 seconds
wall clock time: 65 minutes 50.60 seconds (3950.60 seconds total)