Starting phenix.real_space_refine
on Tue Jul 29 14:42:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_33623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_33623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_33623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_33623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5s_33623/07_2025/7y5s_33623.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B
  Time building chain proxies: 7.10, per 1000 atoms: 0.62
  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: 3.10
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.66
  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: 3.93

  Time building geometry restraints manager: 3.47 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             0.500
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.090
  Find NCS groups from input model:        0.230
  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:             0.010
  Load rotamer database and sin/cos tables:10.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.920
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.001   TRP C 419 
 HIS   0.002   0.001   HIS C 186 
 PHE   0.011   0.001   PHE C 179 
 TYR   0.014   0.001   TYR A 374 
 ARG   0.003   0.000   ARG B 225 

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

*********************** 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  : 1.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 ILE cc_start: 0.6749 (mt) cc_final: 0.6536 (mt)
REVERT: A  289 TYR cc_start: 0.8328 (p90) cc_final: 0.8088 (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: 0.8609 (mt)
REVERT: B  470 THR cc_start: 0.8136 (m) cc_final: 0.7821 (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: 0.7234
  time to fit residues: 259.2918
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  : 1.291 
-------------------------------------------------------------------------------
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 126 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0970
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 136 optimal weight:    0.8980
   overall best weight:    1.3782

-------------------------------------------------------------------------------
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 345 HIS
A 376 GLN
A 402 ASN
A 436 GLN
B  69 ASN
B  89 ASN
B 242 ASN
B 402 ASN
B 436 GLN
C  89 ASN
C 110 GLN
** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 ASN
C 255 GLN
C 290 ASN
** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN
C 402 ASN
** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 436 GLN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.150496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.136248 restraints weight = 15718.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.12
r_work: 0.3693 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3542 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  11820  Z= 0.213
  Angle     :  0.696  11.928  16101  Z= 0.380
  Chirality :  0.053   0.209   1734
  Planarity :  0.006   0.058   2136
  Dihedral  :  6.318  71.009   1654
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.69 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 11.22 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.20), residues: 1509
  helix:  3.91 (0.67), residues: 48
  sheet: -0.24 (0.28), residues: 414
  loop : -2.26 (0.15), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 419 
 HIS   0.008   0.002   HIS B 145 
 PHE   0.028   0.002   PHE B 474 
 TYR   0.016   0.002   TYR A 120 
 ARG   0.011   0.001   ARG C 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  234)
  hydrogen bonds       : angle       6.05298 (  648)
  covalent geometry    : bond        0.00489 (11820)
  covalent geometry    : angle       0.69620 (16101)

*********************** 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
  327 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 276
  time to evaluate  : 1.363 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7788 (ptmt)
REVERT: A  233 VAL cc_start: 0.6638 (p) cc_final: 0.6350 (m)
REVERT: A  264 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6620 (ttm)
REVERT: A  293 HIS cc_start: 0.8079 (m170) cc_final: 0.7804 (m170)
REVERT: A  301 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8194 (m-30)
REVERT: A  399 ASN cc_start: 0.8486 (t0) cc_final: 0.8187 (t0)
REVERT: A  400 SER cc_start: 0.8198 (m) cc_final: 0.7898 (m)
REVERT: A  470 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8274 (p)
REVERT: A  518 GLN cc_start: 0.8200 (mt0) cc_final: 0.7991 (mt0)
REVERT: B   60 ASN cc_start: 0.8043 (m110) cc_final: 0.7718 (m-40)
REVERT: B  110 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7207 (mt0)
REVERT: B  158 VAL cc_start: 0.7583 (t) cc_final: 0.7253 (t)
REVERT: B  160 TRP cc_start: 0.7883 (t60) cc_final: 0.7561 (t60)
REVERT: B  174 LEU cc_start: 0.8054 (mt) cc_final: 0.7827 (mp)
REVERT: B  199 LYS cc_start: 0.8463 (ttpt) cc_final: 0.8262 (ttmt)
REVERT: B  230 ASP cc_start: 0.7852 (m-30) cc_final: 0.7504 (m-30)
REVERT: B  232 ASP cc_start: 0.6836 (m-30) cc_final: 0.6363 (m-30)
REVERT: B  266 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7765 (mtp)
REVERT: B  291 ASN cc_start: 0.8326 (m-40) cc_final: 0.8123 (m110)
REVERT: B  293 HIS cc_start: 0.8208 (m170) cc_final: 0.7797 (m-70)
REVERT: B  319 ASN cc_start: 0.8482 (p0) cc_final: 0.8264 (p0)
REVERT: B  385 LEU cc_start: 0.8993 (mt) cc_final: 0.8713 (mp)
REVERT: B  388 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (m)
REVERT: B  396 ASP cc_start: 0.7377 (t70) cc_final: 0.7064 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8331 (m) cc_final: 0.8069 (m)
REVERT: B  470 THR cc_start: 0.8434 (m) cc_final: 0.8226 (p)
REVERT: B  505 THR cc_start: 0.7968 (m) cc_final: 0.7683 (p)
REVERT: C  102 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6692 (mpt-90)
REVERT: C  115 PHE cc_start: 0.8277 (p90) cc_final: 0.8057 (p90)
REVERT: C  145 HIS cc_start: 0.7666 (p90) cc_final: 0.7438 (p90)
REVERT: C  258 SER cc_start: 0.7268 (OUTLIER) cc_final: 0.6980 (p)
REVERT: C  276 ARG cc_start: 0.8111 (ttp-110) cc_final: 0.7802 (ttm170)
REVERT: C  357 ASP cc_start: 0.8167 (t70) cc_final: 0.7955 (OUTLIER)
REVERT: C  383 ASP cc_start: 0.7734 (t0) cc_final: 0.7528 (t0)
REVERT: C  396 ASP cc_start: 0.7474 (t0) cc_final: 0.7201 (t0)
REVERT: C  400 SER cc_start: 0.8415 (m) cc_final: 0.8179 (m)
REVERT: C  470 THR cc_start: 0.8465 (m) cc_final: 0.8242 (p)
REVERT: C  488 SER cc_start: 0.8651 (t) cc_final: 0.8284 (p)
REVERT: C  518 GLN cc_start: 0.8250 (mt0) cc_final: 0.8037 (mt0)
  outliers start: 51
  outliers final: 20
  residues processed: 298
  average time/residue: 0.9793
  time to fit residues: 327.7836
Evaluate side-chains
  272 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 245
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
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  144 THR
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  352 THR
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 B residue  390 LEU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain C residue   85 THR
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  258 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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 120 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 136 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A  60 ASN
A  89 ASN
A 376 GLN
A 414 ASN
B  89 ASN
B 255 GLN
B 290 ASN
B 414 ASN
C  56 GLN
** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.147707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133764 restraints weight = 16044.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.14
r_work: 0.3665 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11820  Z= 0.178
  Angle     :  0.651   8.971  16101  Z= 0.350
  Chirality :  0.051   0.193   1734
  Planarity :  0.005   0.051   2136
  Dihedral  :  5.798  22.086   1650
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.43 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.20), residues: 1509
  helix:  3.90 (0.67), residues: 48
  sheet: -0.56 (0.26), residues: 429
  loop : -2.20 (0.16), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 419 
 HIS   0.007   0.002   HIS A 245 
 PHE   0.017   0.002   PHE C 474 
 TYR   0.019   0.002   TYR A 395 
 ARG   0.006   0.001   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  234)
  hydrogen bonds       : angle       5.82318 (  648)
  covalent geometry    : bond        0.00406 (11820)
  covalent geometry    : angle       0.65085 (16101)

*********************** 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
  301 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 259
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.7982 (p-80) cc_final: 0.7522 (p-80)
REVERT: A  208 ASN cc_start: 0.8068 (m-40) cc_final: 0.7809 (m-40)
REVERT: A  232 ASP cc_start: 0.6877 (m-30) cc_final: 0.6662 (m-30)
REVERT: A  233 VAL cc_start: 0.6604 (p) cc_final: 0.6389 (m)
REVERT: A  292 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7520 (ptmt)
REVERT: A  293 HIS cc_start: 0.8166 (m170) cc_final: 0.7849 (m170)
REVERT: A  301 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8245 (m-30)
REVERT: A  400 SER cc_start: 0.8240 (m) cc_final: 0.7874 (m)
REVERT: A  434 ARG cc_start: 0.8320 (ptp90) cc_final: 0.7668 (ptt-90)
REVERT: A  510 ASP cc_start: 0.5508 (p0) cc_final: 0.5258 (p0)
REVERT: A  512 ASN cc_start: 0.8377 (m-40) cc_final: 0.8074 (m-40)
REVERT: A  518 GLN cc_start: 0.8291 (mt0) cc_final: 0.8082 (mt0)
REVERT: B   41 VAL cc_start: 0.8146 (p) cc_final: 0.7904 (m)
REVERT: B   83 MET cc_start: 0.6725 (tpp) cc_final: 0.6504 (tpt)
REVERT: B  110 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7270 (mt0)
REVERT: B  158 VAL cc_start: 0.7837 (t) cc_final: 0.7541 (t)
REVERT: B  230 ASP cc_start: 0.7974 (m-30) cc_final: 0.7508 (m-30)
REVERT: B  255 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7278 (tm-30)
REVERT: B  279 SER cc_start: 0.8296 (t) cc_final: 0.8063 (p)
REVERT: B  291 ASN cc_start: 0.8312 (m-40) cc_final: 0.8080 (m110)
REVERT: B  293 HIS cc_start: 0.8152 (m170) cc_final: 0.7686 (m-70)
REVERT: B  319 ASN cc_start: 0.8446 (p0) cc_final: 0.8230 (p0)
REVERT: B  347 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7480 (pp)
REVERT: B  385 LEU cc_start: 0.8973 (mt) cc_final: 0.8718 (OUTLIER)
REVERT: B  388 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8420 (m)
REVERT: B  396 ASP cc_start: 0.7276 (t70) cc_final: 0.6937 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8390 (m) cc_final: 0.8052 (m)
REVERT: B  483 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7995 (ppt-90)
REVERT: C   41 VAL cc_start: 0.8240 (p) cc_final: 0.7957 (m)
REVERT: C  102 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6705 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7619 (p90) cc_final: 0.7352 (p90)
REVERT: C  357 ASP cc_start: 0.8140 (t70) cc_final: 0.7920 (OUTLIER)
REVERT: C  385 LEU cc_start: 0.8955 (mt) cc_final: 0.8568 (mp)
REVERT: C  396 ASP cc_start: 0.7338 (t0) cc_final: 0.7100 (t0)
REVERT: C  400 SER cc_start: 0.8437 (m) cc_final: 0.8235 (m)
REVERT: C  470 THR cc_start: 0.8511 (m) cc_final: 0.8266 (p)
REVERT: C  518 GLN cc_start: 0.8331 (mt0) cc_final: 0.8051 (mt0)
  outliers start: 42
  outliers final: 21
  residues processed: 281
  average time/residue: 0.9541
  time to fit residues: 297.9413
Evaluate side-chains
  269 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 243
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  292 LYS
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 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  255 GLN
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  439 SER
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  483 ARG
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  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  439 SER
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 54 optimal weight:    0.8980
   chunk 116 optimal weight:    0.2980
   chunk 91 optimal weight:    0.1980
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 143 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 114 optimal weight:    0.8980
   chunk 76 optimal weight:    0.0980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
A 290 ASN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 ASN
B 255 GLN
** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
B 422 GLN
C 145 HIS
C 164 ASN
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 = 0.3973 r_free = 0.3973 target = 0.149429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.135569 restraints weight = 15950.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 2.16
r_work: 0.3716 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11820  Z= 0.107
  Angle     :  0.590  13.897  16101  Z= 0.313
  Chirality :  0.049   0.186   1734
  Planarity :  0.004   0.046   2136
  Dihedral  :  5.490  24.940   1650
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 19.14 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.20), residues: 1509
  helix:  3.63 (0.65), residues: 48
  sheet: -0.63 (0.27), residues: 390
  loop : -2.04 (0.16), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 419 
 HIS   0.003   0.001   HIS B 145 
 PHE   0.032   0.001   PHE B 474 
 TYR   0.012   0.001   TYR A 395 
 ARG   0.006   0.000   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02667 (  234)
  hydrogen bonds       : angle       5.37937 (  648)
  covalent geometry    : bond        0.00235 (11820)
  covalent geometry    : angle       0.58976 (16101)

*********************** 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
  295 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 263
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6611 (tpt) cc_final: 0.6072 (tpt)
REVERT: A  145 HIS cc_start: 0.7898 (p-80) cc_final: 0.7594 (p-80)
REVERT: A  232 ASP cc_start: 0.6825 (m-30) cc_final: 0.6520 (m-30)
REVERT: A  253 MET cc_start: 0.5697 (ttm) cc_final: 0.5408 (ttp)
REVERT: A  293 HIS cc_start: 0.8095 (m170) cc_final: 0.7812 (m170)
REVERT: A  396 ASP cc_start: 0.7480 (t0) cc_final: 0.7261 (t0)
REVERT: A  399 ASN cc_start: 0.8499 (t0) cc_final: 0.8186 (t0)
REVERT: A  530 ARG cc_start: 0.7652 (mpp80) cc_final: 0.7262 (mpp80)
REVERT: B   41 VAL cc_start: 0.8165 (p) cc_final: 0.7946 (m)
REVERT: B   60 ASN cc_start: 0.7931 (m110) cc_final: 0.7546 (m-40)
REVERT: B  139 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.5825 (mtt-85)
REVERT: B  158 VAL cc_start: 0.7806 (t) cc_final: 0.7505 (t)
REVERT: B  208 ASN cc_start: 0.8037 (m-40) cc_final: 0.7757 (m110)
REVERT: B  230 ASP cc_start: 0.7803 (m-30) cc_final: 0.7480 (m-30)
REVERT: B  255 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7198 (tm-30)
REVERT: B  266 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7853 (mtp)
REVERT: B  291 ASN cc_start: 0.8242 (m-40) cc_final: 0.8018 (m110)
REVERT: B  293 HIS cc_start: 0.8114 (m170) cc_final: 0.7701 (m-70)
REVERT: B  319 ASN cc_start: 0.8419 (p0) cc_final: 0.8167 (p0)
REVERT: B  346 SER cc_start: 0.7274 (t) cc_final: 0.6844 (p)
REVERT: B  347 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7405 (pp)
REVERT: B  352 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7823 (p)
REVERT: B  388 SER cc_start: 0.8763 (OUTLIER) cc_final: 0.8365 (m)
REVERT: B  396 ASP cc_start: 0.7195 (t70) cc_final: 0.6892 (t0)
REVERT: B  400 SER cc_start: 0.8317 (m) cc_final: 0.7944 (m)
REVERT: B  470 THR cc_start: 0.8532 (p) cc_final: 0.8300 (p)
REVERT: B  519 ASP cc_start: 0.7718 (t0) cc_final: 0.7490 (t0)
REVERT: C   41 VAL cc_start: 0.8245 (p) cc_final: 0.7953 (m)
REVERT: C  102 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6586 (mpt-90)
REVERT: C  228 ASN cc_start: 0.8368 (m-40) cc_final: 0.8157 (m-40)
REVERT: C  272 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7623 (ptt180)
REVERT: C  357 ASP cc_start: 0.8082 (t70) cc_final: 0.7843 (OUTLIER)
REVERT: C  385 LEU cc_start: 0.8893 (mt) cc_final: 0.8551 (mp)
REVERT: C  396 ASP cc_start: 0.7457 (t0) cc_final: 0.7198 (t0)
REVERT: C  398 ASN cc_start: 0.7238 (p0) cc_final: 0.6684 (p0)
REVERT: C  400 SER cc_start: 0.8262 (m) cc_final: 0.7878 (m)
REVERT: C  470 THR cc_start: 0.8542 (m) cc_final: 0.8311 (p)
REVERT: C  481 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7442 (tp)
REVERT: C  518 GLN cc_start: 0.8310 (mt0) cc_final: 0.7999 (mt0)
  outliers start: 32
  outliers final: 15
  residues processed: 276
  average time/residue: 1.4622
  time to fit residues: 447.1320
Evaluate side-chains
  267 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 244
  time to evaluate  : 2.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  266 MET
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  418 ILE
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  266 MET
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 C residue  102 ARG
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  272 ARG
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    0.0970
   chunk 125 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 111 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0370
   chunk 141 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0030
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.4268

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 110 GLN
A 208 ASN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
B 414 ASN
C 164 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.148717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.134936 restraints weight = 16046.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.18
r_work: 0.3722 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11820  Z= 0.109
  Angle     :  0.597  11.939  16101  Z= 0.313
  Chirality :  0.049   0.180   1734
  Planarity :  0.004   0.046   2136
  Dihedral  :  5.386  20.368   1650
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.72 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.20), residues: 1509
  helix:  3.63 (0.65), residues: 48
  sheet: -0.64 (0.27), residues: 369
  loop : -2.07 (0.16), residues: 1092

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 419 
 HIS   0.003   0.001   HIS B 186 
 PHE   0.023   0.001   PHE B 115 
 TYR   0.014   0.001   TYR C 235 
 ARG   0.005   0.000   ARG B 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02598 (  234)
  hydrogen bonds       : angle       5.40922 (  648)
  covalent geometry    : bond        0.00242 (11820)
  covalent geometry    : angle       0.59733 (16101)

*********************** 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
  301 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 259
  time to evaluate  : 2.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.7920 (p-80) cc_final: 0.7562 (p-80)
REVERT: A  156 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5507 (tt0)
REVERT: A  232 ASP cc_start: 0.6759 (m-30) cc_final: 0.6554 (m-30)
REVERT: A  253 MET cc_start: 0.5664 (ttm) cc_final: 0.5444 (ttp)
REVERT: A  262 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7443 (mm)
REVERT: A  292 LYS cc_start: 0.7505 (ptmt) cc_final: 0.7246 (ptmt)
REVERT: A  293 HIS cc_start: 0.8129 (m170) cc_final: 0.7898 (m170)
REVERT: A  301 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8210 (m-30)
REVERT: A  346 SER cc_start: 0.7808 (t) cc_final: 0.7470 (p)
REVERT: A  396 ASP cc_start: 0.7464 (t0) cc_final: 0.7192 (t0)
REVERT: A  400 SER cc_start: 0.8171 (m) cc_final: 0.7811 (m)
REVERT: B   41 VAL cc_start: 0.8169 (p) cc_final: 0.7955 (m)
REVERT: B   60 ASN cc_start: 0.7965 (m110) cc_final: 0.7586 (m-40)
REVERT: B  110 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7268 (mt0)
REVERT: B  156 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5399 (tt0)
REVERT: B  160 TRP cc_start: 0.7998 (t60) cc_final: 0.7709 (t60)
REVERT: B  208 ASN cc_start: 0.8022 (m-40) cc_final: 0.7743 (m110)
REVERT: B  230 ASP cc_start: 0.7721 (m-30) cc_final: 0.7424 (m-30)
REVERT: B  235 TYR cc_start: 0.7801 (m-80) cc_final: 0.7533 (m-80)
REVERT: B  255 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7254 (tm-30)
REVERT: B  266 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7843 (mtp)
REVERT: B  291 ASN cc_start: 0.8185 (m-40) cc_final: 0.7919 (m110)
REVERT: B  293 HIS cc_start: 0.8140 (m170) cc_final: 0.7703 (m-70)
REVERT: B  319 ASN cc_start: 0.8426 (p0) cc_final: 0.8205 (p0)
REVERT: B  346 SER cc_start: 0.7315 (t) cc_final: 0.6919 (p)
REVERT: B  347 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7454 (pp)
REVERT: B  352 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7780 (p)
REVERT: B  383 ASP cc_start: 0.7305 (t0) cc_final: 0.6764 (p0)
REVERT: B  388 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8367 (m)
REVERT: B  396 ASP cc_start: 0.7155 (t70) cc_final: 0.6880 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8275 (m) cc_final: 0.7936 (m)
REVERT: B  470 THR cc_start: 0.8521 (p) cc_final: 0.8303 (p)
REVERT: B  480 THR cc_start: 0.7830 (m) cc_final: 0.7552 (t)
REVERT: B  530 ARG cc_start: 0.7815 (mpp80) cc_final: 0.7554 (mpp80)
REVERT: C   41 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7973 (m)
REVERT: C  102 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6638 (mpt-90)
REVERT: C  331 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7879 (ttt90)
REVERT: C  347 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7713 (pp)
REVERT: C  357 ASP cc_start: 0.8028 (t70) cc_final: 0.7819 (t0)
REVERT: C  368 MET cc_start: 0.8285 (mtp) cc_final: 0.8079 (mtm)
REVERT: C  385 LEU cc_start: 0.8822 (mt) cc_final: 0.8566 (mp)
REVERT: C  396 ASP cc_start: 0.7467 (t0) cc_final: 0.7138 (t0)
REVERT: C  398 ASN cc_start: 0.7150 (p0) cc_final: 0.6594 (p0)
REVERT: C  400 SER cc_start: 0.8249 (m) cc_final: 0.7770 (m)
REVERT: C  470 THR cc_start: 0.8576 (m) cc_final: 0.8336 (p)
REVERT: C  481 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7461 (tp)
REVERT: C  518 GLN cc_start: 0.8361 (mt0) cc_final: 0.8064 (mt0)
  outliers start: 42
  outliers final: 15
  residues processed: 279
  average time/residue: 1.2778
  time to fit residues: 397.1065
Evaluate side-chains
  276 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 248
  time to evaluate  : 2.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  301 ASP
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  418 ILE
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  266 MET
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 C residue   41 VAL
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  323 THR
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 121 optimal weight:    0.8980
   chunk 132 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 129 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 141 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 126 optimal weight:    1.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 110 GLN
A 175 GLN
A 291 ASN
B 255 GLN
B 414 ASN
B 422 GLN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 518 GLN
C 164 ASN
C 291 ASN
C 376 GLN
C 409 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.144137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.130398 restraints weight = 16075.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.13
r_work: 0.3624 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.5167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  11820  Z= 0.200
  Angle     :  0.672  11.366  16101  Z= 0.357
  Chirality :  0.052   0.192   1734
  Planarity :  0.005   0.044   2136
  Dihedral  :  5.824  23.253   1650
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.97 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.20), residues: 1509
  helix:  3.71 (0.68), residues: 48
  sheet: -0.73 (0.27), residues: 378
  loop : -2.11 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 419 
 HIS   0.006   0.002   HIS B 186 
 PHE   0.034   0.002   PHE B 474 
 TYR   0.022   0.002   TYR C 235 
 ARG   0.006   0.001   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03491 (  234)
  hydrogen bonds       : angle       5.95397 (  648)
  covalent geometry    : bond        0.00463 (11820)
  covalent geometry    : angle       0.67236 (16101)

*********************** 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
  296 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 244
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6366 (tpt) cc_final: 0.5975 (tpt)
REVERT: A  145 HIS cc_start: 0.7969 (p-80) cc_final: 0.7708 (p-80)
REVERT: A  262 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7586 (mm)
REVERT: A  293 HIS cc_start: 0.8242 (m170) cc_final: 0.7929 (m170)
REVERT: A  301 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8263 (m-30)
REVERT: A  396 ASP cc_start: 0.7468 (t0) cc_final: 0.7145 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8245 (m) cc_final: 0.7781 (m)
REVERT: A  530 ARG cc_start: 0.7566 (mpp80) cc_final: 0.7169 (mpp80)
REVERT: B   41 VAL cc_start: 0.8309 (p) cc_final: 0.8104 (m)
REVERT: B  139 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.5828 (mtt-85)
REVERT: B  156 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5464 (tt0)
REVERT: B  208 ASN cc_start: 0.7969 (m-40) cc_final: 0.7700 (m110)
REVERT: B  230 ASP cc_start: 0.7880 (m-30) cc_final: 0.7522 (m-30)
REVERT: B  235 TYR cc_start: 0.7911 (m-80) cc_final: 0.7628 (m-80)
REVERT: B  255 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7232 (tm-30)
REVERT: B  279 SER cc_start: 0.8353 (t) cc_final: 0.8137 (p)
REVERT: B  289 TYR cc_start: 0.8325 (p90) cc_final: 0.8004 (p90)
REVERT: B  291 ASN cc_start: 0.8313 (m-40) cc_final: 0.8007 (m110)
REVERT: B  293 HIS cc_start: 0.8236 (m170) cc_final: 0.7754 (m-70)
REVERT: B  319 ASN cc_start: 0.8468 (p0) cc_final: 0.8255 (OUTLIER)
REVERT: B  346 SER cc_start: 0.7379 (t) cc_final: 0.7050 (p)
REVERT: B  347 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7558 (pp)
REVERT: B  388 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8422 (m)
REVERT: B  396 ASP cc_start: 0.7317 (t70) cc_final: 0.7057 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8419 (m) cc_final: 0.8112 (m)
REVERT: B  530 ARG cc_start: 0.7827 (mpp80) cc_final: 0.7558 (mpp80)
REVERT: C   41 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7968 (m)
REVERT: C   43 ASP cc_start: 0.7362 (p0) cc_final: 0.7129 (p0)
REVERT: C  102 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6586 (mpt-90)
REVERT: C  156 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.5091 (tt0)
REVERT: C  258 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6904 (p)
REVERT: C  357 ASP cc_start: 0.7959 (t70) cc_final: 0.7741 (t0)
REVERT: C  385 LEU cc_start: 0.8927 (mt) cc_final: 0.8636 (mp)
REVERT: C  396 ASP cc_start: 0.7537 (t0) cc_final: 0.7121 (t0)
REVERT: C  400 SER cc_start: 0.8468 (m) cc_final: 0.8211 (m)
REVERT: C  470 THR cc_start: 0.8481 (m) cc_final: 0.8235 (p)
REVERT: C  481 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7525 (tm)
REVERT: C  518 GLN cc_start: 0.8376 (mt0) cc_final: 0.8077 (mt0)
REVERT: C  519 ASP cc_start: 0.7859 (t0) cc_final: 0.7578 (t0)
  outliers start: 52
  outliers final: 21
  residues processed: 273
  average time/residue: 0.9384
  time to fit residues: 283.9262
Evaluate side-chains
  266 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  266 MET
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  156 GLU
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  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue  102 ARG
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  323 THR
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Chi-restraints excluded: chain C residue  529 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 135 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 146 optimal weight:    0.7980
   chunk 126 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0670
   overall best weight:    1.1522

-------------------------------------------------------------------------------
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**
B 255 GLN
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 376 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.141118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.127553 restraints weight = 16192.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.13
r_work: 0.3621 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11820  Z= 0.169
  Angle     :  0.654  10.000  16101  Z= 0.345
  Chirality :  0.051   0.190   1734
  Planarity :  0.005   0.050   2136
  Dihedral  :  5.802  22.781   1650
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.71 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.20), residues: 1509
  helix:  3.67 (0.67), residues: 48
  sheet: -0.70 (0.26), residues: 408
  loop : -2.16 (0.16), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 419 
 HIS   0.005   0.002   HIS B 145 
 PHE   0.030   0.002   PHE B 474 
 TYR   0.021   0.001   TYR C 235 
 ARG   0.006   0.001   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03165 (  234)
  hydrogen bonds       : angle       5.86799 (  648)
  covalent geometry    : bond        0.00389 (11820)
  covalent geometry    : angle       0.65428 (16101)

*********************** 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
  296 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 250
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6522 (tpt) cc_final: 0.6155 (tpt)
REVERT: A  262 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7621 (mp)
REVERT: A  293 HIS cc_start: 0.8227 (m170) cc_final: 0.7948 (m170)
REVERT: A  301 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (m-30)
REVERT: A  346 SER cc_start: 0.7783 (t) cc_final: 0.7485 (p)
REVERT: A  396 ASP cc_start: 0.7324 (t0) cc_final: 0.6973 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8254 (m) cc_final: 0.7909 (m)
REVERT: A  526 SER cc_start: 0.7317 (t) cc_final: 0.6997 (p)
REVERT: B   41 VAL cc_start: 0.8336 (p) cc_final: 0.8099 (m)
REVERT: B   52 THR cc_start: 0.7433 (p) cc_final: 0.7057 (p)
REVERT: B  139 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6010 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7970 (m-40) cc_final: 0.7690 (m110)
REVERT: B  230 ASP cc_start: 0.7879 (m-30) cc_final: 0.7511 (m-30)
REVERT: B  235 TYR cc_start: 0.7872 (m-80) cc_final: 0.7577 (m-80)
REVERT: B  255 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7415 (tm-30)
REVERT: B  289 TYR cc_start: 0.8311 (p90) cc_final: 0.8091 (p90)
REVERT: B  291 ASN cc_start: 0.8332 (m-40) cc_final: 0.8010 (m110)
REVERT: B  293 HIS cc_start: 0.8144 (m170) cc_final: 0.7648 (m-70)
REVERT: B  346 SER cc_start: 0.7355 (t) cc_final: 0.7062 (p)
REVERT: B  347 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7586 (pp)
REVERT: B  352 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7854 (p)
REVERT: B  383 ASP cc_start: 0.7451 (t0) cc_final: 0.7096 (p0)
REVERT: B  388 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8453 (m)
REVERT: B  396 ASP cc_start: 0.7215 (t70) cc_final: 0.6965 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8396 (m) cc_final: 0.8095 (m)
REVERT: B  526 SER cc_start: 0.7395 (t) cc_final: 0.7182 (p)
REVERT: B  530 ARG cc_start: 0.7834 (mpp80) cc_final: 0.7536 (mpp80)
REVERT: C   41 VAL cc_start: 0.8326 (OUTLIER) cc_final: 0.8091 (m)
REVERT: C   43 ASP cc_start: 0.7401 (p0) cc_final: 0.7152 (p0)
REVERT: C  156 GLU cc_start: 0.5352 (OUTLIER) cc_final: 0.4960 (tt0)
REVERT: C  185 VAL cc_start: 0.4118 (OUTLIER) cc_final: 0.3846 (t)
REVERT: C  212 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8287 (ptpp)
REVERT: C  258 SER cc_start: 0.7191 (OUTLIER) cc_final: 0.6906 (p)
REVERT: C  385 LEU cc_start: 0.8923 (mt) cc_final: 0.8645 (mp)
REVERT: C  396 ASP cc_start: 0.7478 (t0) cc_final: 0.7009 (t0)
REVERT: C  400 SER cc_start: 0.8468 (m) cc_final: 0.8211 (m)
REVERT: C  470 THR cc_start: 0.8511 (m) cc_final: 0.8272 (p)
REVERT: C  480 THR cc_start: 0.8293 (m) cc_final: 0.7953 (t)
REVERT: C  481 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7522 (tm)
REVERT: C  518 GLN cc_start: 0.8356 (mt0) cc_final: 0.8064 (mt0)
REVERT: C  519 ASP cc_start: 0.7847 (t0) cc_final: 0.7613 (t0)
  outliers start: 46
  outliers final: 24
  residues processed: 280
  average time/residue: 0.8522
  time to fit residues: 265.7352
Evaluate side-chains
  274 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 240
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
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  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 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  280 LEU
Chi-restraints excluded: chain B residue  319 ASN
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  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue   41 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  185 VAL
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  280 LEU
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  323 THR
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 133 optimal weight:    0.9980
   chunk 149 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0050
   overall best weight:    1.0000

-------------------------------------------------------------------------------
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 399 ASN
B 255 GLN
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 376 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.127720 restraints weight = 16117.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.13
r_work: 0.3627 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  11820  Z= 0.156
  Angle     :  0.648  10.758  16101  Z= 0.341
  Chirality :  0.051   0.183   1734
  Planarity :  0.005   0.053   2136
  Dihedral  :  5.813  22.519   1650
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.70 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.20), residues: 1509
  helix:  3.72 (0.67), residues: 48
  sheet: -0.67 (0.27), residues: 378
  loop : -2.13 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 419 
 HIS   0.006   0.001   HIS A 145 
 PHE   0.027   0.002   PHE B 474 
 TYR   0.020   0.001   TYR C 235 
 ARG   0.006   0.001   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03059 (  234)
  hydrogen bonds       : angle       5.85512 (  648)
  covalent geometry    : bond        0.00360 (11820)
  covalent geometry    : angle       0.64799 (16101)

*********************** 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
  295 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 249
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.8104 (p-80) cc_final: 0.7868 (p-80)
REVERT: A  262 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7624 (mp)
REVERT: A  293 HIS cc_start: 0.8211 (m170) cc_final: 0.7955 (m170)
REVERT: A  301 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8365 (m-30)
REVERT: A  346 SER cc_start: 0.7794 (t) cc_final: 0.7497 (p)
REVERT: A  396 ASP cc_start: 0.7473 (t70) cc_final: 0.7064 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8243 (m) cc_final: 0.7897 (m)
REVERT: A  526 SER cc_start: 0.7359 (t) cc_final: 0.6995 (p)
REVERT: B   41 VAL cc_start: 0.8347 (p) cc_final: 0.8111 (m)
REVERT: B   52 THR cc_start: 0.7430 (p) cc_final: 0.7054 (p)
REVERT: B  139 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.5899 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7907 (m-40) cc_final: 0.7652 (m110)
REVERT: B  230 ASP cc_start: 0.7868 (m-30) cc_final: 0.7507 (m-30)
REVERT: B  235 TYR cc_start: 0.7887 (m-80) cc_final: 0.7601 (m-80)
REVERT: B  255 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7272 (tm-30)
REVERT: B  289 TYR cc_start: 0.8337 (p90) cc_final: 0.8119 (p90)
REVERT: B  291 ASN cc_start: 0.8321 (m-40) cc_final: 0.7980 (m110)
REVERT: B  293 HIS cc_start: 0.8169 (m170) cc_final: 0.7704 (m-70)
REVERT: B  346 SER cc_start: 0.7363 (t) cc_final: 0.7071 (p)
REVERT: B  347 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7595 (pp)
REVERT: B  352 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (p)
REVERT: B  383 ASP cc_start: 0.7446 (t0) cc_final: 0.7019 (p0)
REVERT: B  388 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8427 (m)
REVERT: B  396 ASP cc_start: 0.7141 (t70) cc_final: 0.6917 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8391 (m) cc_final: 0.8107 (m)
REVERT: B  526 SER cc_start: 0.7439 (t) cc_final: 0.7192 (p)
REVERT: C   41 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (m)
REVERT: C  156 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4969 (tt0)
REVERT: C  212 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8235 (ptpp)
REVERT: C  258 SER cc_start: 0.7193 (OUTLIER) cc_final: 0.6904 (p)
REVERT: C  385 LEU cc_start: 0.8923 (mt) cc_final: 0.8660 (mp)
REVERT: C  396 ASP cc_start: 0.7492 (t0) cc_final: 0.6996 (t0)
REVERT: C  400 SER cc_start: 0.8476 (m) cc_final: 0.8203 (m)
REVERT: C  470 THR cc_start: 0.8505 (m) cc_final: 0.8270 (p)
REVERT: C  480 THR cc_start: 0.8280 (m) cc_final: 0.7954 (t)
REVERT: C  481 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (tm)
REVERT: C  518 GLN cc_start: 0.8356 (mt0) cc_final: 0.8082 (mt0)
REVERT: C  526 SER cc_start: 0.7495 (t) cc_final: 0.7090 (p)
  outliers start: 46
  outliers final: 25
  residues processed: 275
  average time/residue: 0.8475
  time to fit residues: 260.0695
Evaluate side-chains
  274 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 240
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
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  250 THR
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 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  266 MET
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  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain C residue   41 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  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  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0370
   chunk 39 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 139 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0570
   chunk 144 optimal weight:    0.9980
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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**
B 255 GLN
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
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 = 0.3936 r_free = 0.3936 target = 0.145146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.131582 restraints weight = 16276.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.18
r_work: 0.3680 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.5477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11820  Z= 0.112
  Angle     :  0.618  10.764  16101  Z= 0.323
  Chirality :  0.049   0.176   1734
  Planarity :  0.004   0.048   2136
  Dihedral  :  5.587  20.668   1650
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.20), residues: 1509
  helix:  3.67 (0.66), residues: 48
  sheet: -0.61 (0.27), residues: 393
  loop : -2.14 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 419 
 HIS   0.004   0.001   HIS C 293 
 PHE   0.025   0.001   PHE B 474 
 TYR   0.016   0.001   TYR C 235 
 ARG   0.007   0.000   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02571 (  234)
  hydrogen bonds       : angle       5.61673 (  648)
  covalent geometry    : bond        0.00251 (11820)
  covalent geometry    : angle       0.61750 (16101)

*********************** 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
  287 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 249
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6469 (tpt) cc_final: 0.6213 (tmm)
REVERT: A  301 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8263 (m-30)
REVERT: A  346 SER cc_start: 0.7796 (t) cc_final: 0.7526 (p)
REVERT: A  396 ASP cc_start: 0.7473 (t70) cc_final: 0.7069 (t0)
REVERT: A  400 SER cc_start: 0.8203 (m) cc_final: 0.7851 (m)
REVERT: A  526 SER cc_start: 0.7351 (t) cc_final: 0.6984 (p)
REVERT: B   41 VAL cc_start: 0.8347 (p) cc_final: 0.8114 (m)
REVERT: B   52 THR cc_start: 0.7375 (p) cc_final: 0.6999 (p)
REVERT: B  139 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.5821 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7840 (m-40) cc_final: 0.7567 (m110)
REVERT: B  230 ASP cc_start: 0.7846 (m-30) cc_final: 0.7507 (m-30)
REVERT: B  235 TYR cc_start: 0.7865 (m-80) cc_final: 0.7512 (m-80)
REVERT: B  255 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7545 (tm-30)
REVERT: B  289 TYR cc_start: 0.8305 (p90) cc_final: 0.8067 (p90)
REVERT: B  291 ASN cc_start: 0.8165 (m-40) cc_final: 0.7950 (m-40)
REVERT: B  293 HIS cc_start: 0.8125 (m170) cc_final: 0.7682 (m-70)
REVERT: B  346 SER cc_start: 0.7289 (t) cc_final: 0.6981 (p)
REVERT: B  347 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7555 (pp)
REVERT: B  352 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7805 (p)
REVERT: B  383 ASP cc_start: 0.7393 (t0) cc_final: 0.6936 (p0)
REVERT: B  388 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8395 (m)
REVERT: B  400 SER cc_start: 0.8362 (m) cc_final: 0.8071 (m)
REVERT: B  526 SER cc_start: 0.7336 (t) cc_final: 0.7098 (p)
REVERT: C   41 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8091 (m)
REVERT: C  156 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4931 (tt0)
REVERT: C  185 VAL cc_start: 0.4221 (OUTLIER) cc_final: 0.3994 (t)
REVERT: C  258 SER cc_start: 0.7181 (m) cc_final: 0.6891 (p)
REVERT: C  264 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6174 (tmt)
REVERT: C  272 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.7710 (ptt180)
REVERT: C  368 MET cc_start: 0.8315 (mtp) cc_final: 0.8070 (mtm)
REVERT: C  385 LEU cc_start: 0.8934 (mt) cc_final: 0.8687 (mp)
REVERT: C  396 ASP cc_start: 0.7416 (t0) cc_final: 0.7034 (t0)
REVERT: C  398 ASN cc_start: 0.7349 (p0) cc_final: 0.6814 (p0)
REVERT: C  400 SER cc_start: 0.8376 (m) cc_final: 0.7917 (m)
REVERT: C  470 THR cc_start: 0.8549 (m) cc_final: 0.8309 (p)
REVERT: C  480 THR cc_start: 0.8105 (m) cc_final: 0.7790 (t)
REVERT: C  518 GLN cc_start: 0.8334 (mt0) cc_final: 0.8085 (mt0)
  outliers start: 38
  outliers final: 22
  residues processed: 270
  average time/residue: 0.8949
  time to fit residues: 269.1090
Evaluate side-chains
  274 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 242
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
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  250 THR
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  418 ILE
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  266 MET
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  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue   41 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  185 VAL
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  455 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 129 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0970
   chunk 102 optimal weight:    0.7980
   chunk 111 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
B 255 GLN
B 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.143808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.130038 restraints weight = 16190.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.23
r_work: 0.3658 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.5538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11820  Z= 0.131
  Angle     :  0.623  10.837  16101  Z= 0.327
  Chirality :  0.050   0.175   1734
  Planarity :  0.005   0.047   2136
  Dihedral  :  5.597  20.735   1650
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 23.60 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.20), residues: 1509
  helix:  3.67 (0.66), residues: 48
  sheet: -0.60 (0.27), residues: 393
  loop : -2.14 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 419 
 HIS   0.004   0.001   HIS C 293 
 PHE   0.033   0.002   PHE C 115 
 TYR   0.016   0.001   TYR C 235 
 ARG   0.007   0.001   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02765 (  234)
  hydrogen bonds       : angle       5.65450 (  648)
  covalent geometry    : bond        0.00302 (11820)
  covalent geometry    : angle       0.62315 (16101)

********************** 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
  278 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 244
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 HIS cc_start: 0.8173 (m170) cc_final: 0.7965 (m-70)
REVERT: A  301 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8336 (m-30)
REVERT: A  346 SER cc_start: 0.7839 (t) cc_final: 0.7551 (p)
REVERT: A  396 ASP cc_start: 0.7540 (t70) cc_final: 0.7119 (t0)
REVERT: A  400 SER cc_start: 0.8221 (m) cc_final: 0.7856 (m)
REVERT: A  518 GLN cc_start: 0.8312 (mt0) cc_final: 0.8076 (pt0)
REVERT: A  526 SER cc_start: 0.7377 (t) cc_final: 0.6983 (p)
REVERT: B   41 VAL cc_start: 0.8349 (p) cc_final: 0.8122 (m)
REVERT: B   52 THR cc_start: 0.7462 (p) cc_final: 0.7080 (p)
REVERT: B  110 GLN cc_start: 0.7533 (mt0) cc_final: 0.7289 (mt0)
REVERT: B  139 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.5815 (mtt-85)
REVERT: B  142 TRP cc_start: 0.6962 (p90) cc_final: 0.6449 (p90)
REVERT: B  208 ASN cc_start: 0.7828 (m-40) cc_final: 0.7534 (m110)
REVERT: B  230 ASP cc_start: 0.7934 (m-30) cc_final: 0.7579 (m-30)
REVERT: B  235 TYR cc_start: 0.7875 (m-80) cc_final: 0.7535 (m-80)
REVERT: B  253 MET cc_start: 0.5665 (ptm) cc_final: 0.5368 (ttp)
REVERT: B  255 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7715 (tm-30)
REVERT: B  291 ASN cc_start: 0.8162 (m-40) cc_final: 0.7948 (m-40)
REVERT: B  293 HIS cc_start: 0.8119 (m170) cc_final: 0.7659 (m-70)
REVERT: B  346 SER cc_start: 0.7403 (t) cc_final: 0.7101 (p)
REVERT: B  347 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7597 (pp)
REVERT: B  352 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7836 (p)
REVERT: B  383 ASP cc_start: 0.7379 (t0) cc_final: 0.6998 (p0)
REVERT: B  388 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8378 (m)
REVERT: B  396 ASP cc_start: 0.7137 (t70) cc_final: 0.6815 (t0)
REVERT: B  400 SER cc_start: 0.8385 (m) cc_final: 0.8100 (m)
REVERT: B  405 MET cc_start: 0.7633 (mtp) cc_final: 0.7418 (mtp)
REVERT: B  526 SER cc_start: 0.7386 (t) cc_final: 0.7087 (p)
REVERT: C   41 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8083 (m)
REVERT: C  102 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6548 (mpt-90)
REVERT: C  156 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4901 (tt0)
REVERT: C  258 SER cc_start: 0.7221 (m) cc_final: 0.6913 (p)
REVERT: C  264 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6315 (tmt)
REVERT: C  385 LEU cc_start: 0.8879 (mt) cc_final: 0.8642 (mp)
REVERT: C  396 ASP cc_start: 0.7472 (t0) cc_final: 0.7068 (t0)
REVERT: C  398 ASN cc_start: 0.7285 (p0) cc_final: 0.6733 (p0)
REVERT: C  400 SER cc_start: 0.8415 (m) cc_final: 0.7943 (m)
REVERT: C  470 THR cc_start: 0.8553 (m) cc_final: 0.8296 (p)
  outliers start: 34
  outliers final: 19
  residues processed: 266
  average time/residue: 0.9023
  time to fit residues: 267.9736
Evaluate side-chains
  265 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 236
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
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  250 THR
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 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  266 MET
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  385 LEU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain C residue   41 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  264 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 79 optimal weight:    6.9990
   chunk 140 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 376 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.138933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.125482 restraints weight = 16231.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.15
r_work: 0.3610 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3458 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.5784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11820  Z= 0.217
  Angle     :  0.700  10.792  16101  Z= 0.373
  Chirality :  0.053   0.198   1734
  Planarity :  0.006   0.047   2136
  Dihedral  :  6.016  23.643   1650
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 23.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.20), residues: 1509
  helix:  3.54 (0.68), residues: 48
  sheet: -0.71 (0.27), residues: 393
  loop : -2.19 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 419 
 HIS   0.006   0.002   HIS C 195 
 PHE   0.034   0.002   PHE C 115 
 TYR   0.024   0.002   TYR C 235 
 ARG   0.007   0.001   ARG A 225 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  234)
  hydrogen bonds       : angle       6.07892 (  648)
  covalent geometry    : bond        0.00508 (11820)
  covalent geometry    : angle       0.70019 (16101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8781.73 seconds
wall clock time: 159 minutes 57.12 seconds (9597.12 seconds total)