Starting phenix.real_space_refine
on Wed May 14 05:46:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y5s_33623/05_2025/7y5s_33623.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y5s_33623/05_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_33623/05_2025/7y5s_33623.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y5s_33623/05_2025/7y5s_33623.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y5s_33623/05_2025/7y5s_33623.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y5s_33623/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.97, per 1000 atoms: 0.52
  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: 2.35
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.86
  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: 4.32

  Time building geometry restraints manager: 2.77 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: 0.08
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:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     26.980
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.110
-------------------------------------------------------------------------------
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  : 1.244 
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: 0.7697
  time to fit residues: 275.4301
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  : 1.162 
-------------------------------------------------------------------------------
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 = 32)----------------|
| 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  : 1.254 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7789 (ptmt)
REVERT: A  233 VAL cc_start: 0.6638 (p) cc_final: 0.6351 (m)
REVERT: A  264 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6623 (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: 0.8193 (m-30)
REVERT: A  399 ASN cc_start: 0.8485 (t0) cc_final: 0.8185 (t0)
REVERT: A  400 SER cc_start: 0.8195 (m) cc_final: 0.7895 (m)
REVERT: A  470 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8277 (p)
REVERT: A  518 GLN cc_start: 0.8198 (mt0) cc_final: 0.7988 (mt0)
REVERT: B   60 ASN cc_start: 0.8042 (m110) cc_final: 0.7719 (m-40)
REVERT: B  110 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7205 (mt0)
REVERT: B  158 VAL cc_start: 0.7584 (t) cc_final: 0.7253 (t)
REVERT: B  160 TRP cc_start: 0.7884 (t60) cc_final: 0.7561 (t60)
REVERT: B  174 LEU cc_start: 0.8058 (mt) cc_final: 0.7831 (mp)
REVERT: B  199 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8263 (ttmt)
REVERT: B  230 ASP cc_start: 0.7854 (m-30) cc_final: 0.7505 (m-30)
REVERT: B  232 ASP cc_start: 0.6837 (m-30) cc_final: 0.6364 (m-30)
REVERT: B  266 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7767 (mtp)
REVERT: B  291 ASN cc_start: 0.8325 (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: 0.8481 (p0) cc_final: 0.8263 (p0)
REVERT: B  385 LEU cc_start: 0.8993 (mt) cc_final: 0.8712 (mp)
REVERT: B  388 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8525 (m)
REVERT: B  396 ASP cc_start: 0.7383 (t70) cc_final: 0.7068 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8330 (m) cc_final: 0.8068 (m)
REVERT: B  470 THR cc_start: 0.8434 (m) cc_final: 0.8226 (p)
REVERT: B  505 THR cc_start: 0.7969 (m) cc_final: 0.7685 (p)
REVERT: C  102 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6695 (mpt-90)
REVERT: C  115 PHE cc_start: 0.8278 (p90) cc_final: 0.8058 (p90)
REVERT: C  145 HIS cc_start: 0.7667 (p90) cc_final: 0.7439 (p90)
REVERT: C  258 SER cc_start: 0.7269 (OUTLIER) cc_final: 0.6981 (p)
REVERT: C  276 ARG cc_start: 0.8109 (ttp-110) cc_final: 0.7802 (ttm170)
REVERT: C  357 ASP cc_start: 0.8169 (t70) cc_final: 0.7955 (OUTLIER)
REVERT: C  383 ASP cc_start: 0.7732 (t0) cc_final: 0.7525 (t0)
REVERT: C  396 ASP cc_start: 0.7478 (t0) cc_final: 0.7204 (t0)
REVERT: C  400 SER cc_start: 0.8416 (m) cc_final: 0.8179 (m)
REVERT: C  470 THR cc_start: 0.8467 (m) cc_final: 0.8244 (p)
REVERT: C  488 SER cc_start: 0.8650 (t) cc_final: 0.8283 (p)
REVERT: C  518 GLN cc_start: 0.8247 (mt0) cc_final: 0.8036 (mt0)
  outliers start: 51
  outliers final: 20
  residues processed: 298
  average time/residue: 0.8023
  time to fit residues: 268.2170
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  : 1.112 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 137 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 136 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 175 GLN
A 290 ASN
A 376 GLN
A 414 ASN
B  89 ASN
B 255 GLN
B 290 ASN
B 414 ASN
** 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: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.146077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.132243 restraints weight = 16031.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.13
r_work: 0.3644 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4557

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= 0.197
  Angle     :  0.673   9.451  16101  Z= 0.363
  Chirality :  0.052   0.211   1734
  Planarity :  0.005   0.050   2136
  Dihedral  :  5.916  22.961   1650
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.51 %
    Favored  : 80.78 %
  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: -2.15 (0.20), residues: 1509
  helix:  3.90 (0.67), residues: 48
  sheet: -0.61 (0.26), residues: 429
  loop : -2.21 (0.16), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 419 
 HIS   0.009   0.002   HIS A 245 
 PHE   0.017   0.002   PHE C 474 
 TYR   0.019   0.002   TYR A 395 
 ARG   0.008   0.001   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  234)
  hydrogen bonds       : angle       5.96709 (  648)
  covalent geometry    : bond        0.00452 (11820)
  covalent geometry    : angle       0.67336 (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
  306 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 261
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TRP cc_start: 0.6886 (p90) cc_final: 0.6634 (p90)
REVERT: A  145 HIS cc_start: 0.7975 (p-80) cc_final: 0.7560 (p-80)
REVERT: A  208 ASN cc_start: 0.8071 (m-40) cc_final: 0.7802 (m-40)
REVERT: A  223 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7812 (mtm-85)
REVERT: A  232 ASP cc_start: 0.6897 (m-30) cc_final: 0.6697 (m-30)
REVERT: A  233 VAL cc_start: 0.6591 (p) cc_final: 0.6362 (m)
REVERT: A  293 HIS cc_start: 0.8178 (m170) cc_final: 0.7855 (m170)
REVERT: A  301 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8244 (m-30)
REVERT: A  400 SER cc_start: 0.8221 (m) cc_final: 0.7863 (m)
REVERT: A  518 GLN cc_start: 0.8321 (mt0) cc_final: 0.8051 (mt0)
REVERT: B   41 VAL cc_start: 0.8195 (p) cc_final: 0.7962 (m)
REVERT: B   83 MET cc_start: 0.6813 (tpp) cc_final: 0.6591 (tpt)
REVERT: B  110 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7279 (mt0)
REVERT: B  158 VAL cc_start: 0.7903 (t) cc_final: 0.7610 (t)
REVERT: B  199 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8260 (ttmt)
REVERT: B  208 ASN cc_start: 0.7992 (m-40) cc_final: 0.7699 (m-40)
REVERT: B  230 ASP cc_start: 0.7971 (m-30) cc_final: 0.7513 (m-30)
REVERT: B  255 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7304 (tm-30)
REVERT: B  279 SER cc_start: 0.8393 (t) cc_final: 0.8191 (p)
REVERT: B  291 ASN cc_start: 0.8322 (m-40) cc_final: 0.8082 (m110)
REVERT: B  293 HIS cc_start: 0.8208 (m170) cc_final: 0.7744 (m-70)
REVERT: B  319 ASN cc_start: 0.8456 (p0) cc_final: 0.8241 (p0)
REVERT: B  347 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7454 (pp)
REVERT: B  385 LEU cc_start: 0.8985 (mt) cc_final: 0.8720 (mp)
REVERT: B  388 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8464 (m)
REVERT: B  396 ASP cc_start: 0.7284 (t70) cc_final: 0.6949 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8403 (m) cc_final: 0.8080 (m)
REVERT: C   41 VAL cc_start: 0.8246 (p) cc_final: 0.7994 (m)
REVERT: C   43 ASP cc_start: 0.7303 (p0) cc_final: 0.7037 (p0)
REVERT: C  102 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6717 (mpt-90)
REVERT: C  145 HIS cc_start: 0.7593 (p90) cc_final: 0.7319 (p90)
REVERT: C  160 TRP cc_start: 0.7838 (t60) cc_final: 0.7175 (t-100)
REVERT: C  357 ASP cc_start: 0.8127 (t70) cc_final: 0.7906 (OUTLIER)
REVERT: C  385 LEU cc_start: 0.8949 (mt) cc_final: 0.8594 (mp)
REVERT: C  396 ASP cc_start: 0.7344 (t0) cc_final: 0.7112 (t0)
REVERT: C  409 ASN cc_start: 0.7734 (m-40) cc_final: 0.7514 (m110)
REVERT: C  470 THR cc_start: 0.8513 (m) cc_final: 0.8262 (p)
REVERT: C  518 GLN cc_start: 0.8350 (mt0) cc_final: 0.7973 (mt0)
  outliers start: 45
  outliers final: 21
  residues processed: 283
  average time/residue: 0.8769
  time to fit residues: 275.9073
Evaluate side-chains
  262 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 237
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
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  301 ASP
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  464 VAL
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 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:    4.9990
   chunk 116 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 143 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 GLN
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
B 414 ASN
B 422 GLN
C  56 GLN
C 145 HIS
C 164 ASN
C 376 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.147205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.133360 restraints weight = 15904.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.15
r_work: 0.3659 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3508 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11820  Z= 0.141
  Angle     :  0.627  12.780  16101  Z= 0.332
  Chirality :  0.050   0.184   1734
  Planarity :  0.005   0.045   2136
  Dihedral  :  5.756  24.205   1650
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 19.22 %
    Favored  : 77.89 %
  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 (0.19), residues: 1509
  helix:  3.59 (0.66), residues: 48
  sheet: -0.63 (0.27), residues: 348
  loop : -2.07 (0.16), residues: 1113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 419 
 HIS   0.004   0.001   HIS C 195 
 PHE   0.031   0.002   PHE B 474 
 TYR   0.015   0.001   TYR C 235 
 ARG   0.005   0.000   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03090 (  234)
  hydrogen bonds       : angle       5.68673 (  648)
  covalent geometry    : bond        0.00321 (11820)
  covalent geometry    : angle       0.62697 (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
  277 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 242
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.7934 (p-80) cc_final: 0.7547 (p-80)
REVERT: A  208 ASN cc_start: 0.8075 (m-40) cc_final: 0.7831 (m-40)
REVERT: A  253 MET cc_start: 0.5801 (ttm) cc_final: 0.5500 (ttp)
REVERT: A  292 LYS cc_start: 0.7707 (ptmt) cc_final: 0.7432 (ptmt)
REVERT: A  293 HIS cc_start: 0.8173 (m170) cc_final: 0.7864 (m170)
REVERT: A  301 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8277 (m-30)
REVERT: A  396 ASP cc_start: 0.7452 (t0) cc_final: 0.7245 (t0)
REVERT: A  399 ASN cc_start: 0.8555 (t0) cc_final: 0.8236 (t0)
REVERT: A  518 GLN cc_start: 0.8335 (mt0) cc_final: 0.8088 (mt0)
REVERT: A  530 ARG cc_start: 0.7614 (mpp80) cc_final: 0.7222 (mpp80)
REVERT: B   41 VAL cc_start: 0.8221 (p) cc_final: 0.8014 (m)
REVERT: B  139 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.5972 (mtt-85)
REVERT: B  199 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8267 (ttmt)
REVERT: B  208 ASN cc_start: 0.7992 (m-40) cc_final: 0.7701 (m110)
REVERT: B  230 ASP cc_start: 0.7902 (m-30) cc_final: 0.7508 (m-30)
REVERT: B  231 ILE cc_start: 0.6742 (mm) cc_final: 0.6531 (mm)
REVERT: B  279 SER cc_start: 0.8331 (t) cc_final: 0.8117 (p)
REVERT: B  291 ASN cc_start: 0.8317 (m-40) cc_final: 0.8035 (m110)
REVERT: B  293 HIS cc_start: 0.8127 (m170) cc_final: 0.7673 (m-70)
REVERT: B  319 ASN cc_start: 0.8464 (p0) cc_final: 0.8221 (p0)
REVERT: B  388 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8446 (m)
REVERT: B  396 ASP cc_start: 0.7324 (t70) cc_final: 0.6991 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8404 (m) cc_final: 0.8068 (m)
REVERT: B  470 THR cc_start: 0.8505 (p) cc_final: 0.8300 (p)
REVERT: B  519 ASP cc_start: 0.7793 (t0) cc_final: 0.7558 (t0)
REVERT: B  530 ARG cc_start: 0.7699 (mpp80) cc_final: 0.7468 (mpp80)
REVERT: C   41 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.8014 (m)
REVERT: C   43 ASP cc_start: 0.7299 (p0) cc_final: 0.7030 (p0)
REVERT: C  102 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6623 (mpt-90)
REVERT: C  357 ASP cc_start: 0.8064 (t70) cc_final: 0.7855 (t0)
REVERT: C  385 LEU cc_start: 0.8895 (mt) cc_final: 0.8501 (mp)
REVERT: C  396 ASP cc_start: 0.7462 (t0) cc_final: 0.7124 (t0)
REVERT: C  409 ASN cc_start: 0.7672 (m-40) cc_final: 0.7455 (m110)
REVERT: C  470 THR cc_start: 0.8525 (m) cc_final: 0.8295 (p)
REVERT: C  481 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7460 (tm)
REVERT: C  518 GLN cc_start: 0.8332 (mt0) cc_final: 0.7979 (mt0)
  outliers start: 35
  outliers final: 16
  residues processed: 262
  average time/residue: 0.8457
  time to fit residues: 247.1592
Evaluate side-chains
  255 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 234
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  368 MET
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  266 MET
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  109 THR
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  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:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 111 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 141 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0670
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 ASN
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 219 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 = 0.3885 r_free = 0.3885 target = 0.143918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.130252 restraints weight = 15892.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.11
r_work: 0.3620 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.5147

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= 0.194
  Angle     :  0.666  10.470  16101  Z= 0.354
  Chirality :  0.052   0.198   1734
  Planarity :  0.005   0.045   2136
  Dihedral  :  5.906  22.985   1650
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.81 %
    Favored  : 77.15 %
  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: -2.26 (0.19), residues: 1509
  helix:  3.54 (0.67), residues: 48
  sheet: -0.72 (0.27), residues: 363
  loop : -2.19 (0.16), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 419 
 HIS   0.005   0.002   HIS C 195 
 PHE   0.024   0.002   PHE B 474 
 TYR   0.019   0.002   TYR C 235 
 ARG   0.007   0.001   ARG A 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  234)
  hydrogen bonds       : angle       5.93476 (  648)
  covalent geometry    : bond        0.00446 (11820)
  covalent geometry    : angle       0.66584 (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
  290 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 241
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6408 (tpt) cc_final: 0.5999 (tpt)
REVERT: A  145 HIS cc_start: 0.7925 (p-80) cc_final: 0.7653 (p-80)
REVERT: A  156 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.5491 (tt0)
REVERT: A  250 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7453 (t)
REVERT: A  262 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7629 (mm)
REVERT: A  293 HIS cc_start: 0.8201 (m170) cc_final: 0.7910 (m170)
REVERT: A  301 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8249 (m-30)
REVERT: A  396 ASP cc_start: 0.7307 (t0) cc_final: 0.7068 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8281 (m) cc_final: 0.7865 (m)
REVERT: A  530 ARG cc_start: 0.7521 (mpp80) cc_final: 0.7178 (mpp80)
REVERT: B   41 VAL cc_start: 0.8318 (p) cc_final: 0.8076 (m)
REVERT: B   52 THR cc_start: 0.7426 (p) cc_final: 0.7078 (p)
REVERT: B  199 LYS cc_start: 0.8564 (tttt) cc_final: 0.8336 (ttmt)
REVERT: B  208 ASN cc_start: 0.8019 (m-40) cc_final: 0.7725 (m110)
REVERT: B  230 ASP cc_start: 0.7915 (m-30) cc_final: 0.7496 (m-30)
REVERT: B  231 ILE cc_start: 0.6722 (mm) cc_final: 0.6522 (mm)
REVERT: B  255 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7250 (tm-30)
REVERT: B  289 TYR cc_start: 0.8279 (p90) cc_final: 0.8050 (p90)
REVERT: B  291 ASN cc_start: 0.8331 (m-40) cc_final: 0.8045 (m110)
REVERT: B  293 HIS cc_start: 0.8211 (m170) cc_final: 0.7742 (m-70)
REVERT: B  319 ASN cc_start: 0.8482 (p0) cc_final: 0.8247 (OUTLIER)
REVERT: B  383 ASP cc_start: 0.7600 (t0) cc_final: 0.7209 (p0)
REVERT: B  388 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8491 (m)
REVERT: B  396 ASP cc_start: 0.7288 (t70) cc_final: 0.6975 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8425 (m) cc_final: 0.8105 (m)
REVERT: B  483 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7456 (ppt-90)
REVERT: B  519 ASP cc_start: 0.7836 (t0) cc_final: 0.7609 (t0)
REVERT: B  530 ARG cc_start: 0.7813 (mpp80) cc_final: 0.7513 (mpp80)
REVERT: C   41 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8094 (m)
REVERT: C   43 ASP cc_start: 0.7399 (p0) cc_final: 0.7121 (p0)
REVERT: C  102 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6539 (mpt-90)
REVERT: C  156 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.5202 (tt0)
REVERT: C  346 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7677 (p)
REVERT: C  357 ASP cc_start: 0.8054 (t70) cc_final: 0.7847 (t0)
REVERT: C  385 LEU cc_start: 0.8848 (mt) cc_final: 0.8585 (mp)
REVERT: C  396 ASP cc_start: 0.7522 (t0) cc_final: 0.7135 (t0)
REVERT: C  409 ASN cc_start: 0.7675 (m-40) cc_final: 0.7460 (m110)
REVERT: C  470 THR cc_start: 0.8484 (m) cc_final: 0.8247 (p)
REVERT: C  480 THR cc_start: 0.8317 (m) cc_final: 0.7956 (t)
REVERT: C  481 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7564 (tm)
REVERT: C  483 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.6788 (ptt-90)
REVERT: C  518 GLN cc_start: 0.8370 (mt0) cc_final: 0.8046 (mt0)
  outliers start: 49
  outliers final: 25
  residues processed: 271
  average time/residue: 0.8693
  time to fit residues: 262.1885
Evaluate side-chains
  264 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 229
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
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  250 THR
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  322 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  409 ASN
Chi-restraints excluded: chain A residue  476 MET
Chi-restraints excluded: chain B residue  109 THR
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  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  483 ARG
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  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  346 SER
Chi-restraints excluded: chain C residue  347 ILE
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  378 ASN
Chi-restraints excluded: chain C residue  387 THR
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  481 LEU
Chi-restraints excluded: chain C residue  483 ARG
Chi-restraints excluded: chain C residue  529 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:    0.6980
   chunk 132 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 129 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 126 optimal weight:    0.8980
   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 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 255 GLN
B 414 ASN
B 422 GLN
** 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 = 0.3924 r_free = 0.3924 target = 0.146889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.133212 restraints weight = 16064.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.14
r_work: 0.3662 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11820  Z= 0.128
  Angle     :  0.622  11.805  16101  Z= 0.327
  Chirality :  0.050   0.175   1734
  Planarity :  0.005   0.046   2136
  Dihedral  :  5.714  22.313   1650
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 19.64 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.20 (0.19), residues: 1509
  helix:  3.49 (0.66), residues: 48
  sheet: -0.59 (0.27), residues: 333
  loop : -2.14 (0.16), residues: 1128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 419 
 HIS   0.004   0.001   HIS B 186 
 PHE   0.020   0.001   PHE B 474 
 TYR   0.015   0.001   TYR C 235 
 ARG   0.006   0.000   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  234)
  hydrogen bonds       : angle       5.64799 (  648)
  covalent geometry    : bond        0.00290 (11820)
  covalent geometry    : angle       0.62192 (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
  292 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 248
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 HIS cc_start: 0.7964 (p-80) cc_final: 0.7702 (p-80)
REVERT: A  262 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7688 (mm)
REVERT: A  301 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8297 (m-30)
REVERT: A  396 ASP cc_start: 0.7459 (t70) cc_final: 0.7154 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8281 (m) cc_final: 0.7828 (m)
REVERT: B   41 VAL cc_start: 0.8331 (p) cc_final: 0.8094 (m)
REVERT: B   52 THR cc_start: 0.7408 (p) cc_final: 0.7031 (p)
REVERT: B  139 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.5938 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7973 (m-40) cc_final: 0.7697 (m110)
REVERT: B  230 ASP cc_start: 0.7837 (m-30) cc_final: 0.7486 (m-30)
REVERT: B  291 ASN cc_start: 0.8298 (m-40) cc_final: 0.7989 (m110)
REVERT: B  293 HIS cc_start: 0.8141 (m170) cc_final: 0.7662 (m-70)
REVERT: B  319 ASN cc_start: 0.8449 (p0) cc_final: 0.8228 (p0)
REVERT: B  352 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7820 (p)
REVERT: B  388 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8443 (m)
REVERT: B  396 ASP cc_start: 0.7268 (t70) cc_final: 0.6981 (t0)
REVERT: B  400 SER cc_start: 0.8378 (m) cc_final: 0.8089 (m)
REVERT: B  447 TRP cc_start: 0.8285 (m100) cc_final: 0.8017 (m100)
REVERT: B  483 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7681 (ppt-90)
REVERT: B  530 ARG cc_start: 0.7751 (mpp80) cc_final: 0.7425 (mpp80)
REVERT: C   41 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8076 (m)
REVERT: C  156 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.5167 (tt0)
REVERT: C  385 LEU cc_start: 0.8847 (mt) cc_final: 0.8594 (mp)
REVERT: C  396 ASP cc_start: 0.7386 (t0) cc_final: 0.6973 (t0)
REVERT: C  409 ASN cc_start: 0.7657 (m-40) cc_final: 0.7432 (m110)
REVERT: C  410 ILE cc_start: 0.8566 (mt) cc_final: 0.8340 (mt)
REVERT: C  470 THR cc_start: 0.8495 (m) cc_final: 0.8270 (p)
REVERT: C  480 THR cc_start: 0.8207 (m) cc_final: 0.7883 (t)
REVERT: C  481 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7512 (tm)
REVERT: C  518 GLN cc_start: 0.8342 (mt0) cc_final: 0.8051 (mt0)
  outliers start: 44
  outliers final: 19
  residues processed: 274
  average time/residue: 0.8891
  time to fit residues: 270.4977
Evaluate side-chains
  261 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 234
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
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  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  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  483 ARG
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 135 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 146 optimal weight:    0.7980
   chunk 126 optimal weight:    0.8980
   chunk 134 optimal weight:    0.0980
   chunk 69 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 110 GLN
A 159 ASN
** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 399 ASN
B 414 ASN
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 219 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 = 0.3927 r_free = 0.3927 target = 0.147117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133450 restraints weight = 16145.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.16
r_work: 0.3664 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3513 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  11820  Z= 0.127
  Angle     :  0.622  10.253  16101  Z= 0.326
  Chirality :  0.050   0.176   1734
  Planarity :  0.005   0.049   2136
  Dihedral  :  5.620  20.532   1650
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.45 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.15 (0.20), residues: 1509
  helix:  3.55 (0.66), residues: 48
  sheet: -0.64 (0.27), residues: 378
  loop : -2.12 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 419 
 HIS   0.004   0.001   HIS B 145 
 PHE   0.018   0.001   PHE B 474 
 TYR   0.016   0.001   TYR C 235 
 ARG   0.007   0.000   ARG C 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02797 (  234)
  hydrogen bonds       : angle       5.58268 (  648)
  covalent geometry    : bond        0.00288 (11820)
  covalent geometry    : angle       0.62154 (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
  278 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 239
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6472 (tpt) cc_final: 0.6144 (tmm)
REVERT: A  262 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7700 (mm)
REVERT: A  293 HIS cc_start: 0.8196 (m170) cc_final: 0.7960 (m170)
REVERT: A  301 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8344 (m-30)
REVERT: A  346 SER cc_start: 0.7807 (t) cc_final: 0.7472 (p)
REVERT: A  396 ASP cc_start: 0.7490 (t70) cc_final: 0.7146 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8260 (m) cc_final: 0.7909 (m)
REVERT: B   41 VAL cc_start: 0.8336 (p) cc_final: 0.8128 (m)
REVERT: B  139 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.5855 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7944 (m-40) cc_final: 0.7663 (m110)
REVERT: B  230 ASP cc_start: 0.7797 (m-30) cc_final: 0.7492 (m-30)
REVERT: B  289 TYR cc_start: 0.8252 (p90) cc_final: 0.7996 (p90)
REVERT: B  291 ASN cc_start: 0.8297 (m-40) cc_final: 0.8051 (m110)
REVERT: B  352 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7822 (p)
REVERT: B  383 ASP cc_start: 0.7606 (t0) cc_final: 0.7208 (p0)
REVERT: B  388 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8418 (m)
REVERT: B  396 ASP cc_start: 0.7151 (t70) cc_final: 0.6889 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8374 (m) cc_final: 0.8082 (m)
REVERT: B  447 TRP cc_start: 0.8262 (m100) cc_final: 0.8002 (m100)
REVERT: B  483 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7685 (ppt-90)
REVERT: B  530 ARG cc_start: 0.7736 (mpp80) cc_final: 0.7417 (mpp80)
REVERT: C   41 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8116 (m)
REVERT: C  156 GLU cc_start: 0.5409 (OUTLIER) cc_final: 0.5143 (tt0)
REVERT: C  346 SER cc_start: 0.7869 (t) cc_final: 0.7619 (p)
REVERT: C  385 LEU cc_start: 0.8848 (mt) cc_final: 0.8589 (mp)
REVERT: C  396 ASP cc_start: 0.7382 (t0) cc_final: 0.6929 (t0)
REVERT: C  409 ASN cc_start: 0.7616 (m-40) cc_final: 0.7290 (m110)
REVERT: C  470 THR cc_start: 0.8514 (m) cc_final: 0.8280 (p)
REVERT: C  480 THR cc_start: 0.8134 (m) cc_final: 0.7823 (t)
REVERT: C  481 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7511 (tm)
REVERT: C  518 GLN cc_start: 0.8318 (mt0) cc_final: 0.8027 (mt0)
  outliers start: 39
  outliers final: 22
  residues processed: 264
  average time/residue: 0.8710
  time to fit residues: 255.1241
Evaluate side-chains
  258 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 229
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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  347 ILE
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  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  483 ARG
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 133 optimal weight:    0.8980
   chunk 149 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 109 optimal weight:    0.3980
   chunk 123 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 291 ASN
C 376 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.140355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.126993 restraints weight = 16019.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.10
r_work: 0.3610 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.5568

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= 0.173
  Angle     :  0.655  10.884  16101  Z= 0.346
  Chirality :  0.051   0.183   1734
  Planarity :  0.005   0.049   2136
  Dihedral  :  5.844  23.015   1650
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.19 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.22 (0.20), residues: 1509
  helix:  3.55 (0.68), residues: 48
  sheet: -0.70 (0.27), residues: 378
  loop : -2.17 (0.16), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 419 
 HIS   0.006   0.001   HIS A 145 
 PHE   0.016   0.002   PHE C 179 
 TYR   0.012   0.001   TYR A 235 
 ARG   0.006   0.001   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  234)
  hydrogen bonds       : angle       5.87696 (  648)
  covalent geometry    : bond        0.00400 (11820)
  covalent geometry    : angle       0.65477 (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
  291 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 248
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.6632 (tpt) cc_final: 0.6420 (tmm)
REVERT: A  253 MET cc_start: 0.5558 (ptm) cc_final: 0.5252 (ttp)
REVERT: A  262 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7872 (mm)
REVERT: A  293 HIS cc_start: 0.8208 (m170) cc_final: 0.7961 (m170)
REVERT: A  301 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8372 (m-30)
REVERT: A  396 ASP cc_start: 0.7535 (t70) cc_final: 0.7146 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8203 (m) cc_final: 0.7806 (m)
REVERT: A  526 SER cc_start: 0.7395 (t) cc_final: 0.6968 (p)
REVERT: B  139 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.5881 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7954 (m-40) cc_final: 0.7650 (m110)
REVERT: B  230 ASP cc_start: 0.7862 (m-30) cc_final: 0.7533 (m-30)
REVERT: B  231 ILE cc_start: 0.6678 (mm) cc_final: 0.6449 (mm)
REVERT: B  289 TYR cc_start: 0.8269 (p90) cc_final: 0.8027 (p90)
REVERT: B  383 ASP cc_start: 0.7574 (t0) cc_final: 0.7172 (p0)
REVERT: B  388 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8470 (m)
REVERT: B  396 ASP cc_start: 0.7173 (t70) cc_final: 0.6933 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8409 (m) cc_final: 0.8126 (m)
REVERT: B  447 TRP cc_start: 0.8273 (m100) cc_final: 0.7973 (m100)
REVERT: B  483 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7827 (ppt-90)
REVERT: B  526 SER cc_start: 0.7353 (t) cc_final: 0.7096 (p)
REVERT: B  530 ARG cc_start: 0.7707 (mpp80) cc_final: 0.7372 (mpp80)
REVERT: C   41 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8083 (m)
REVERT: C   83 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6556 (tpt)
REVERT: C  156 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.5132 (tt0)
REVERT: C  258 SER cc_start: 0.7185 (m) cc_final: 0.6899 (p)
REVERT: C  346 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7700 (p)
REVERT: C  385 LEU cc_start: 0.8918 (mt) cc_final: 0.8676 (mp)
REVERT: C  396 ASP cc_start: 0.7416 (t0) cc_final: 0.6975 (t0)
REVERT: C  470 THR cc_start: 0.8506 (m) cc_final: 0.8271 (p)
REVERT: C  480 THR cc_start: 0.8259 (m) cc_final: 0.7936 (t)
REVERT: C  518 GLN cc_start: 0.8352 (mt0) cc_final: 0.8060 (mt0)
REVERT: C  526 SER cc_start: 0.7434 (t) cc_final: 0.7041 (p)
  outliers start: 43
  outliers final: 22
  residues processed: 278
  average time/residue: 0.8162
  time to fit residues: 253.3872
Evaluate side-chains
  267 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 238
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  483 ARG
Chi-restraints excluded: chain C residue   41 VAL
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  102 ARG
Chi-restraints excluded: chain C residue  156 GLU
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  346 SER
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  455 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 105 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   chunk 139 optimal weight:    0.0270
   chunk 71 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 144 optimal weight:    0.9980
   overall best weight:    0.9040

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 309 HIS
B 228 ASN
B 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 164 ASN
C 291 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 = 0.3899 r_free = 0.3899 target = 0.145063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.131519 restraints weight = 16183.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.14
r_work: 0.3640 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.5622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11820  Z= 0.147
  Angle     :  0.645  10.659  16101  Z= 0.340
  Chirality :  0.051   0.182   1734
  Planarity :  0.005   0.048   2136
  Dihedral  :  5.778  22.156   1650
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.44 %
    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: -2.18 (0.20), residues: 1509
  helix:  3.48 (0.68), residues: 48
  sheet: -0.66 (0.27), residues: 378
  loop : -2.15 (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   0.015   0.001   PHE B 115 
 TYR   0.013   0.001   TYR A 235 
 ARG   0.007   0.001   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02957 (  234)
  hydrogen bonds       : angle       5.78704 (  648)
  covalent geometry    : bond        0.00339 (11820)
  covalent geometry    : angle       0.64454 (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
  283 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 244
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7688 (p) cc_final: 0.7331 (p)
REVERT: A  253 MET cc_start: 0.5410 (ptm) cc_final: 0.5176 (ttp)
REVERT: A  262 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7870 (mm)
REVERT: A  293 HIS cc_start: 0.8177 (m170) cc_final: 0.7937 (m170)
REVERT: A  301 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (m-30)
REVERT: A  396 ASP cc_start: 0.7503 (t70) cc_final: 0.7104 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8235 (m) cc_final: 0.7917 (m)
REVERT: A  526 SER cc_start: 0.7417 (t) cc_final: 0.7011 (p)
REVERT: B   41 VAL cc_start: 0.8401 (m) cc_final: 0.8104 (p)
REVERT: B   52 THR cc_start: 0.7485 (p) cc_final: 0.7144 (p)
REVERT: B  139 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.5832 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7929 (m-40) cc_final: 0.7637 (m110)
REVERT: B  230 ASP cc_start: 0.7847 (m-30) cc_final: 0.7478 (m-30)
REVERT: B  352 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7833 (p)
REVERT: B  383 ASP cc_start: 0.7552 (t0) cc_final: 0.7133 (p0)
REVERT: B  388 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8459 (m)
REVERT: B  396 ASP cc_start: 0.7089 (t70) cc_final: 0.6846 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8395 (m) cc_final: 0.8114 (m)
REVERT: B  483 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7844 (ppt-90)
REVERT: B  526 SER cc_start: 0.7387 (t) cc_final: 0.7128 (p)
REVERT: B  530 ARG cc_start: 0.7677 (mpp80) cc_final: 0.7350 (mpp80)
REVERT: C   41 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8104 (m)
REVERT: C  156 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.5092 (tt0)
REVERT: C  346 SER cc_start: 0.7910 (t) cc_final: 0.7676 (p)
REVERT: C  385 LEU cc_start: 0.8917 (mt) cc_final: 0.8637 (mp)
REVERT: C  396 ASP cc_start: 0.7410 (t0) cc_final: 0.6919 (t0)
REVERT: C  409 ASN cc_start: 0.7621 (m-40) cc_final: 0.7413 (m110)
REVERT: C  470 THR cc_start: 0.8531 (m) cc_final: 0.8291 (p)
REVERT: C  480 THR cc_start: 0.8300 (m) cc_final: 0.7970 (t)
REVERT: C  518 GLN cc_start: 0.8355 (mt0) cc_final: 0.8108 (mt0)
REVERT: C  526 SER cc_start: 0.7451 (t) cc_final: 0.7059 (p)
  outliers start: 39
  outliers final: 25
  residues processed: 270
  average time/residue: 0.8023
  time to fit residues: 242.4490
Evaluate side-chains
  268 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 237
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
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  280 LEU
Chi-restraints excluded: chain B residue  347 ILE
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  483 ARG
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  156 GLU
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  344 LEU
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:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 126 optimal weight:    0.5980
   chunk 118 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0370
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.0660

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3878 r_free = 0.3878 target = 0.140574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.127396 restraints weight = 16179.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 2.10
r_work: 0.3622 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3474 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.5734

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= 0.164
  Angle     :  0.658  10.934  16101  Z= 0.347
  Chirality :  0.051   0.190   1734
  Planarity :  0.005   0.048   2136
  Dihedral  :  5.838  22.297   1650
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.43 %
    Favored  : 73.68 %
  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:  3.52 (0.68), residues: 48
  sheet: -0.75 (0.27), residues: 384
  loop : -2.16 (0.16), residues: 1077

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 419 
 HIS   0.005   0.001   HIS C 186 
 PHE   0.015   0.002   PHE B 115 
 TYR   0.013   0.001   TYR A 235 
 ARG   0.007   0.001   ARG A 223 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03166 (  234)
  hydrogen bonds       : angle       5.82428 (  648)
  covalent geometry    : bond        0.00379 (11820)
  covalent geometry    : angle       0.65831 (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
  274 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 239
  time to evaluate  : 1.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 THR cc_start: 0.7763 (p) cc_final: 0.7433 (p)
REVERT: A   83 MET cc_start: 0.6655 (tpt) cc_final: 0.6453 (tmm)
REVERT: A  253 MET cc_start: 0.5384 (ptm) cc_final: 0.5141 (ttp)
REVERT: A  262 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7890 (mm)
REVERT: A  301 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (m-30)
REVERT: A  396 ASP cc_start: 0.7561 (t70) cc_final: 0.7158 (OUTLIER)
REVERT: A  400 SER cc_start: 0.8196 (m) cc_final: 0.7812 (m)
REVERT: A  526 SER cc_start: 0.7455 (t) cc_final: 0.7032 (p)
REVERT: B   41 VAL cc_start: 0.8417 (m) cc_final: 0.8100 (p)
REVERT: B   52 THR cc_start: 0.7553 (p) cc_final: 0.7227 (p)
REVERT: B  139 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.5873 (mtt-85)
REVERT: B  208 ASN cc_start: 0.7956 (m-40) cc_final: 0.7628 (m110)
REVERT: B  230 ASP cc_start: 0.7873 (m-30) cc_final: 0.7479 (m-30)
REVERT: B  289 TYR cc_start: 0.8237 (p90) cc_final: 0.7949 (p90)
REVERT: B  383 ASP cc_start: 0.7556 (t0) cc_final: 0.7133 (p0)
REVERT: B  388 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8454 (m)
REVERT: B  396 ASP cc_start: 0.7113 (t70) cc_final: 0.6890 (OUTLIER)
REVERT: B  400 SER cc_start: 0.8368 (m) cc_final: 0.8106 (m)
REVERT: B  483 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7865 (ppt-90)
REVERT: B  526 SER cc_start: 0.7422 (t) cc_final: 0.7175 (p)
REVERT: B  530 ARG cc_start: 0.7695 (mpp80) cc_final: 0.7353 (mpp80)
REVERT: C   41 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (m)
REVERT: C  156 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5279 (tt0)
REVERT: C  346 SER cc_start: 0.7914 (t) cc_final: 0.7671 (p)
REVERT: C  385 LEU cc_start: 0.8910 (mt) cc_final: 0.8703 (mp)
REVERT: C  396 ASP cc_start: 0.7421 (t0) cc_final: 0.6967 (t0)
REVERT: C  409 ASN cc_start: 0.7624 (m-40) cc_final: 0.7416 (m110)
REVERT: C  470 THR cc_start: 0.8578 (m) cc_final: 0.8326 (p)
REVERT: C  480 THR cc_start: 0.8259 (m) cc_final: 0.7955 (t)
REVERT: C  518 GLN cc_start: 0.8408 (mt0) cc_final: 0.8161 (mt0)
REVERT: C  526 SER cc_start: 0.7530 (t) cc_final: 0.7128 (p)
  outliers start: 35
  outliers final: 24
  residues processed: 264
  average time/residue: 0.8721
  time to fit residues: 257.5857
Evaluate side-chains
  264 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  156 GLU
Chi-restraints excluded: chain A residue  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  280 LEU
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  439 SER
Chi-restraints excluded: chain B residue  483 ARG
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  156 GLU
Chi-restraints excluded: chain C residue  258 SER
Chi-restraints excluded: chain C residue  301 ASP
Chi-restraints excluded: chain C residue  344 LEU
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 101 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 140 optimal weight:    0.0020
   chunk 107 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
A 291 ASN
B 164 ASN
B 255 GLN
** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 ASN
** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3910 r_free = 0.3910 target = 0.143180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.130091 restraints weight = 16203.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.10
r_work: 0.3669 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11820  Z= 0.124
  Angle     :  0.631  10.958  16101  Z= 0.332
  Chirality :  0.050   0.184   1734
  Planarity :  0.005   0.057   2136
  Dihedral  :  5.666  20.348   1650
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.43 %
    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: -2.14 (0.20), residues: 1509
  helix:  3.49 (0.68), residues: 48
  sheet: -0.39 (0.28), residues: 363
  loop : -2.20 (0.16), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 419 
 HIS   0.004   0.001   HIS C 186 
 PHE   0.014   0.001   PHE B 115 
 TYR   0.018   0.001   TYR A 284 
 ARG   0.006   0.000   ARG C 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02777 (  234)
  hydrogen bonds       : angle       5.61132 (  648)
  covalent geometry    : bond        0.00284 (11820)
  covalent geometry    : angle       0.63095 (16101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7601.92 seconds
wall clock time: 131 minutes 36.00 seconds (7896.00 seconds total)