Starting phenix.real_space_refine
on Wed Mar  4 09:27:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xyc_33519/03_2026/7xyc_33519.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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    7944      2.51       5
     N    2148      2.21       5
     O    2475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12621
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 562, 4207
          Classifications: {'peptide': 562}
          Link IDs: {'PTRANS': 16, 'TRANS': 545}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 3.27, per 1000 atoms: 0.26
  Number of scatterers: 12621
  At special positions: 0
  Unit cell: (91.26, 90.09, 136.89, 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    2475      8.00
     N    2148      7.00
     C    7944      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 523.2 milliseconds
  

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3012

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 27 sheets defined
      6.2% alpha, 21.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP A 390 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'B' and resid 21 through 28
    Processing helix  chain 'B' and resid 89 through 91
      No H-bonds generated for 'chain 'B' and resid 89 through 91'
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER B 114 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP B 390 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
    Processing helix  chain 'C' and resid 21 through 28
    Processing helix  chain 'C' and resid 89 through 91
      No H-bonds generated for 'chain 'C' and resid 89 through 91'
    Processing helix  chain 'C' and resid 101 through 114
      removed outlier: 3.857A  pdb=" N   SER C 114 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.574A  pdb=" N   ASP C 390 " --> pdb=" O   GLN C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 426
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP A  17 " --> pdb=" O   PHE A  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU A  53 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE A  86 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY A 198 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ARG A 231 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU A 199 " --> pdb=" O   ARG A 231 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE A 230 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 151
    Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 184
      removed outlier: 6.133A  pdb=" N   LEU A 183 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR A 216 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR A 242 " --> pdb=" O   THR A 216 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE A 218 " --> pdb=" O   TYR A 242 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   ILE A 239 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR A 272 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   PHE A 241 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   PHE A 291 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR A 316 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET A 293 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LEU A 318 " --> pdb=" O   MET A 293 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE A 295 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   VAL A 313 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ASN A 345 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL A 315 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL A 347 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA A 317 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE A 344 " --> pdb=" O   ASN A 373 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   SER A 375 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL A 346 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE A 372 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   SER A 406 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A 374 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE A 223 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 246 " --> pdb=" O   GLN A 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE A 284 " --> pdb=" O   THR A 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE A 305 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE A 334 " --> pdb=" O   HIS A 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL A 476 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR A 559 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY A 522 " --> pdb=" O   TYR A 513 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 455 through 456
      removed outlier: 3.727A  pdb=" N   LEU A 456 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR A 567 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE A 570 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER A 494 " --> pdb=" O   ILE A 570 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP B  17 " --> pdb=" O   PHE B  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU B  53 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE B  86 " --> pdb=" O   PHE B 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY B 198 " --> pdb=" O   TYR B 160 " (cutoff:3.500A)
      removed outlier: 8.669A  pdb=" N   ARG B 231 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU B 199 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 230 " --> pdb=" O   TYR B 257 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 149 through 151
    Processing sheet with id=AB5, first strand: chain 'B' and resid 183 through 184
      removed outlier: 6.133A  pdb=" N   LEU B 183 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR B 216 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR B 242 " --> pdb=" O   THR B 216 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE B 218 " --> pdb=" O   TYR B 242 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE B 239 " --> pdb=" O   THR B 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR B 272 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   PHE B 241 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   PHE B 291 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR B 316 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET B 293 " --> pdb=" O   THR B 316 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   LEU B 318 " --> pdb=" O   MET B 293 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   PHE B 295 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   VAL B 313 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   ASN B 345 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL B 315 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL B 347 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA B 317 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE B 344 " --> pdb=" O   ASN B 373 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   SER B 375 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B 346 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE B 372 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   SER B 406 " --> pdb=" O   ILE B 372 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B 374 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE B 223 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER B 246 " --> pdb=" O   GLN B 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE B 305 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE B 334 " --> pdb=" O   HIS B 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL B 476 " --> pdb=" O   THR B 559 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   THR B 559 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY B 522 " --> pdb=" O   TYR B 513 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 455 through 456
      removed outlier: 3.728A  pdb=" N   LEU B 456 " --> pdb=" O   VAL B 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR B 567 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE B 570 " --> pdb=" O   SER B 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER B 494 " --> pdb=" O   ILE B 570 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 17 through 19
      removed outlier: 6.352A  pdb=" N   TRP C  17 " --> pdb=" O   PHE C  39 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   LEU C  53 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87
      removed outlier: 6.755A  pdb=" N   ILE C  86 " --> pdb=" O   PHE C 120 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 136
      removed outlier: 7.116A  pdb=" N   GLY C 198 " --> pdb=" O   TYR C 160 " (cutoff:3.500A)
      removed outlier: 8.670A  pdb=" N   ARG C 231 " --> pdb=" O   SER C 197 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   LEU C 199 " --> pdb=" O   ARG C 231 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ILE C 230 " --> pdb=" O   TYR C 257 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 151
    Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 184
      removed outlier: 6.132A  pdb=" N   LEU C 183 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   THR C 216 " --> pdb=" O   VAL C 240 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   TYR C 242 " --> pdb=" O   THR C 216 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE C 218 " --> pdb=" O   TYR C 242 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   ILE C 239 " --> pdb=" O   THR C 270 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   TYR C 272 " --> pdb=" O   ILE C 239 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   PHE C 241 " --> pdb=" O   TYR C 272 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   PHE C 291 " --> pdb=" O   SER C 314 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   THR C 316 " --> pdb=" O   PHE C 291 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   MET C 293 " --> pdb=" O   THR C 316 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   LEU C 318 " --> pdb=" O   MET C 293 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   PHE C 295 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   VAL C 313 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ASN C 345 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL C 315 " --> pdb=" O   ASN C 345 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL C 347 " --> pdb=" O   VAL C 315 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA C 317 " --> pdb=" O   VAL C 347 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   PHE C 344 " --> pdb=" O   ASN C 373 " (cutoff:3.500A)
      removed outlier: 7.862A  pdb=" N   SER C 375 " --> pdb=" O   PHE C 344 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL C 346 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE C 372 " --> pdb=" O   SER C 404 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   SER C 406 " --> pdb=" O   ILE C 372 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   LEU C 374 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 222 through 224
      removed outlier: 6.866A  pdb=" N   PHE C 223 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER C 246 " --> pdb=" O   GLN C 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'C' and resid 284 through 286
      removed outlier: 5.994A  pdb=" N   ILE C 284 " --> pdb=" O   THR C 306 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   PHE C 305 " --> pdb=" O   GLU C 335 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ILE C 334 " --> pdb=" O   HIS C 365 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'C' and resid 442 through 445
      removed outlier: 3.754A  pdb=" N   VAL C 476 " --> pdb=" O   THR C 559 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   THR C 559 " --> pdb=" O   VAL C 476 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLY C 522 " --> pdb=" O   TYR C 513 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 455 through 456
      removed outlier: 3.727A  pdb=" N   LEU C 456 " --> pdb=" O   VAL C 466 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   TYR C 567 " --> pdb=" O   LEU C 467 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE C 570 " --> pdb=" O   SER C 494 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   SER C 494 " --> pdb=" O   ILE C 570 " (cutoff:3.500A)

    210 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.35

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4143
        1.35 -     1.46: 3170
        1.46 -     1.58: 5500
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 12888
  Sorted by residual:
  bond pdb=" CA  TYR B 176 "
       pdb=" CB  TYR B 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.19e+00
  bond pdb=" CA  TYR C 176 "
       pdb=" CB  TYR C 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.18e+00
  bond pdb=" CA  TYR A 176 "
       pdb=" CB  TYR A 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.548 -0.024 1.62e-02 3.81e+03 2.17e+00
  bond pdb=" N   GLY B 233 "
       pdb=" CA  GLY B 233 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.008 7.70e-03 1.69e+04 1.10e+00
  bond pdb=" N   GLY A 233 "
       pdb=" CA  GLY A 233 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.008 7.70e-03 1.69e+04 1.08e+00
  ... (remaining 12883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 16816
        1.32 -     2.64: 537
        2.64 -     3.95: 117
        3.95 -     5.27: 44
        5.27 -     6.59: 15
  Bond angle restraints: 17529
  Sorted by residual:
  angle pdb=" CA  ILE C 268 "
        pdb=" CB  ILE C 268 "
        pdb=" CG2 ILE C 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.24   -4.74 1.70e+00 3.46e-01 7.78e+00
  angle pdb=" CA  ILE A 268 "
        pdb=" CB  ILE A 268 "
        pdb=" CG2 ILE A 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.24   -4.74 1.70e+00 3.46e-01 7.76e+00
  angle pdb=" CA  ILE B 268 "
        pdb=" CB  ILE B 268 "
        pdb=" CG2 ILE B 268 "
      ideal   model   delta    sigma   weight residual
     110.50  115.23   -4.73 1.70e+00 3.46e-01 7.74e+00
  angle pdb=" C   ASP C 263 "
        pdb=" N   ASP C 264 "
        pdb=" CA  ASP C 264 "
      ideal   model   delta    sigma   weight residual
     121.54  126.80   -5.26 1.91e+00 2.74e-01 7.59e+00
  angle pdb=" C   SER C 447 "
        pdb=" CA  SER C 447 "
        pdb=" CB  SER C 447 "
      ideal   model   delta    sigma   weight residual
     110.42  115.89   -5.47 1.99e+00 2.53e-01 7.55e+00
  ... (remaining 17524 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.50: 6752
       16.50 -    32.99: 540
       32.99 -    49.49: 127
       49.49 -    65.99: 9
       65.99 -    82.48: 30
  Dihedral angle restraints: 7458
    sinusoidal: 2685
      harmonic: 4773
  Sorted by residual:
  dihedral pdb=" CA  LYS B 115 "
           pdb=" C   LYS B 115 "
           pdb=" N   LEU B 116 "
           pdb=" CA  LEU B 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.96  -15.04     0      5.00e+00 4.00e-02 9.05e+00
  dihedral pdb=" CA  LYS A 115 "
           pdb=" C   LYS A 115 "
           pdb=" N   LEU A 116 "
           pdb=" CA  LEU A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.98  -15.02     0      5.00e+00 4.00e-02 9.02e+00
  dihedral pdb=" CA  LYS C 115 "
           pdb=" C   LYS C 115 "
           pdb=" N   LEU C 116 "
           pdb=" CA  LEU C 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.02  -14.98     0      5.00e+00 4.00e-02 8.98e+00
  ... (remaining 7455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1584
       0.054 -    0.108: 327
       0.108 -    0.162: 72
       0.162 -    0.216: 0
       0.216 -    0.270: 3
  Chirality restraints: 1986
  Sorted by residual:
  chirality pdb=" CB  ILE C 268 "
            pdb=" CA  ILE C 268 "
            pdb=" CG1 ILE C 268 "
            pdb=" CG2 ILE C 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.83e+00
  chirality pdb=" CB  ILE B 268 "
            pdb=" CA  ILE B 268 "
            pdb=" CG1 ILE B 268 "
            pdb=" CG2 ILE B 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  ILE A 268 "
            pdb=" CA  ILE A 268 "
            pdb=" CG1 ILE A 268 "
            pdb=" CG2 ILE A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1983 not shown)

  Planarity restraints: 2268
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 448 "   -0.052 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO C 449 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO C 449 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 449 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 448 "   -0.052 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO A 449 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 448 "    0.052 5.00e-02 4.00e+02   7.96e-02 1.01e+01
        pdb=" N   PRO B 449 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.043 5.00e-02 4.00e+02
  ... (remaining 2265 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2059
        2.77 -     3.30: 12265
        3.30 -     3.83: 20182
        3.83 -     4.37: 23268
        4.37 -     4.90: 41722
  Nonbonded interactions: 99496
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 205 "
            pdb=" OD1 ASP A 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR B 205 "
            pdb=" OD1 ASP B 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR C 205 "
            pdb=" OD1 ASP C 207 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE C 336 "
            pdb=" OG  SER C 367 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE B 336 "
            pdb=" OG  SER B 367 "
     model   vdw
     2.289 3.040
  ... (remaining 99491 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.840
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
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      :  0.002   0.030  12888  Z= 0.122
  Angle     :  0.631   6.591  17529  Z= 0.341
  Chirality :  0.046   0.270   1986
  Planarity :  0.004   0.080   2268
  Dihedral  : 13.853  82.483   4446
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.14 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.18), residues: 1680
  helix:  2.87 (0.70), residues: 63
  sheet:  0.40 (0.23), residues: 462
  loop : -2.30 (0.15), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 543 
 TYR   0.018   0.001   TYR B 176 
 PHE   0.014   0.001   PHE C 300 
 TRP   0.015   0.001   TRP B 237 
 HIS   0.004   0.001   HIS B 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (12888)
  covalent geometry    : angle       0.63088 (17529)
  hydrogen bonds       : bond        0.16902 (  210)
  hydrogen bonds       : angle       4.75533 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  375 SER cc_start: 0.8872 (m) cc_final: 0.8669 (m)
REVERT: A  454 GLU cc_start: 0.7415 (pp20) cc_final: 0.7094 (pt0)
REVERT: B   83 ASP cc_start: 0.7604 (t0) cc_final: 0.7384 (t0)
REVERT: B  375 SER cc_start: 0.8956 (m) cc_final: 0.8658 (m)
REVERT: C   83 ASP cc_start: 0.7412 (t0) cc_final: 0.7054 (t0)
REVERT: C  268 ILE cc_start: 0.8651 (tp) cc_final: 0.8450 (tp)
REVERT: C  454 GLU cc_start: 0.7466 (pp20) cc_final: 0.7094 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0887
  time to fit residues: 29.7356
Evaluate side-chains
  150 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    0.0020
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    6.9990
   overall best weight:    1.0992

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 370 ASN
A 387 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN
B 387 GLN
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 370 ASN
C 387 GLN
C 414 ASN
** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.112509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.096694 restraints weight = 18976.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.097675 restraints weight = 15198.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.098525 restraints weight = 12952.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.098813 restraints weight = 11558.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.098813 restraints weight = 10816.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12888  Z= 0.135
  Angle     :  0.596   5.858  17529  Z= 0.313
  Chirality :  0.048   0.240   1986
  Planarity :  0.003   0.055   2268
  Dihedral  :  4.375  17.134   1812
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  9.94 %
    Favored  : 88.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.19), residues: 1680
  helix:  2.69 (0.71), residues: 63
  sheet: -0.08 (0.22), residues: 582
  loop : -2.21 (0.16), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 238 
 TYR   0.018   0.001   TYR B 176 
 PHE   0.008   0.001   PHE A 322 
 TRP   0.014   0.001   TRP C 237 
 HIS   0.004   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12888)
  covalent geometry    : angle       0.59592 (17529)
  hydrogen bonds       : bond        0.03378 (  210)
  hydrogen bonds       : angle       4.69044 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  454 GLU cc_start: 0.7821 (pp20) cc_final: 0.7226 (pp20)
REVERT: B   83 ASP cc_start: 0.7590 (t0) cc_final: 0.7375 (t70)
REVERT: B  224 ASP cc_start: 0.8351 (p0) cc_final: 0.8143 (p0)
REVERT: B  232 MET cc_start: 0.8622 (mmt) cc_final: 0.8262 (mmt)
REVERT: B  370 ASN cc_start: 0.8135 (m-40) cc_final: 0.7892 (m110)
REVERT: B  375 SER cc_start: 0.9053 (m) cc_final: 0.8827 (m)
REVERT: C   83 ASP cc_start: 0.7610 (t0) cc_final: 0.7274 (t0)
REVERT: C  232 MET cc_start: 0.8632 (mmt) cc_final: 0.8431 (mmt)
REVERT: C  268 ILE cc_start: 0.8963 (tp) cc_final: 0.8761 (tp)
REVERT: C  454 GLU cc_start: 0.7736 (pp20) cc_final: 0.7118 (pp20)
  outliers start: 17
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0782
  time to fit residues: 22.1392
Evaluate side-chains
  146 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  343 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 160 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 112 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
A 566 GLN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 283 ASN
C 414 ASN
C 566 GLN
** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.100987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.081899 restraints weight = 19903.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.082915 restraints weight = 14055.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.084294 restraints weight = 13197.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.084872 restraints weight = 9848.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.084957 restraints weight = 9077.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  12888  Z= 0.288
  Angle     :  0.710   6.111  17529  Z= 0.383
  Chirality :  0.052   0.289   1986
  Planarity :  0.004   0.039   2268
  Dihedral  :  5.341  19.541   1812
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.16 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.19), residues: 1680
  helix:  0.63 (0.63), residues: 81
  sheet: -0.45 (0.22), residues: 573
  loop : -2.44 (0.16), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 238 
 TYR   0.023   0.002   TYR B 176 
 PHE   0.014   0.002   PHE A 276 
 TRP   0.030   0.002   TRP B 237 
 HIS   0.007   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 (12888)
  covalent geometry    : angle       0.71043 (17529)
  hydrogen bonds       : bond        0.04844 (  210)
  hydrogen bonds       : angle       5.57452 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 143
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A   43 TRP cc_start: 0.9187 (t60) cc_final: 0.8582 (t60)
REVERT: A  180 SER cc_start: 0.9313 (p) cc_final: 0.9045 (m)
REVERT: A  189 PHE cc_start: 0.7706 (m-80) cc_final: 0.7404 (m-10)
REVERT: A  508 GLN cc_start: 0.8613 (tp40) cc_final: 0.8293 (tp40)
REVERT: B  180 SER cc_start: 0.9279 (p) cc_final: 0.8926 (m)
REVERT: B  232 MET cc_start: 0.8876 (mmt) cc_final: 0.8118 (mmt)
REVERT: C   28 PHE cc_start: 0.8720 (t80) cc_final: 0.8358 (t80)
REVERT: C   83 ASP cc_start: 0.7917 (t0) cc_final: 0.7621 (t0)
REVERT: C  180 SER cc_start: 0.9289 (p) cc_final: 0.9032 (m)
REVERT: C  189 PHE cc_start: 0.7756 (m-80) cc_final: 0.7521 (m-10)
REVERT: C  238 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7717 (mtp-110)
REVERT: C  508 GLN cc_start: 0.8595 (tp40) cc_final: 0.8271 (tp40)
  outliers start: 53
  outliers final: 42
  residues processed: 180
  average time/residue: 0.0888
  time to fit residues: 25.5635
Evaluate side-chains
  166 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 124
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   74 ASP
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  235 ASN
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  235 ASN
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  334 ILE
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  565 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 152 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 102 optimal weight:    7.9990
   chunk 107 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0020
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN
B 468 HIS
** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
C 566 GLN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 573 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.108072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.089920 restraints weight = 19197.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.090840 restraints weight = 16018.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.091785 restraints weight = 12670.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.092380 restraints weight = 10800.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.092789 restraints weight = 9301.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12888  Z= 0.112
  Angle     :  0.572   6.155  17529  Z= 0.303
  Chirality :  0.047   0.268   1986
  Planarity :  0.003   0.030   2268
  Dihedral  :  4.705  19.137   1812
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.01 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.19), residues: 1680
  helix:  0.87 (0.65), residues: 81
  sheet: -0.51 (0.22), residues: 588
  loop : -2.30 (0.17), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  80 
 TYR   0.023   0.001   TYR B 176 
 PHE   0.011   0.001   PHE B 322 
 TRP   0.018   0.001   TRP A 237 
 HIS   0.007   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (12888)
  covalent geometry    : angle       0.57236 (17529)
  hydrogen bonds       : bond        0.02875 (  210)
  hydrogen bonds       : angle       4.87132 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 136
  time to evaluate  : 0.461 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9127 (p) cc_final: 0.8793 (m)
REVERT: A  200 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8694 (tt)
REVERT: B  180 SER cc_start: 0.9264 (p) cc_final: 0.8844 (m)
REVERT: B  232 MET cc_start: 0.8780 (mmt) cc_final: 0.8144 (mmt)
REVERT: C   83 ASP cc_start: 0.7741 (t0) cc_final: 0.7466 (t0)
REVERT: C  180 SER cc_start: 0.9225 (p) cc_final: 0.8912 (m)
REVERT: C  268 ILE cc_start: 0.9080 (tp) cc_final: 0.8839 (tp)
  outliers start: 54
  outliers final: 38
  residues processed: 178
  average time/residue: 0.0774
  time to fit residues: 23.1055
Evaluate side-chains
  170 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 154 optimal weight:    0.0170
   chunk 93 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 137 optimal weight:    0.9990
   chunk 161 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.2422

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

Flipped N/Q/H residues before XYZ refinement:
** A  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 414 ASN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 573 ASN
C 414 ASN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.105198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.087462 restraints weight = 19517.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.088404 restraints weight = 15445.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.089331 restraints weight = 14626.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.089840 restraints weight = 11197.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.089935 restraints weight = 10549.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12888  Z= 0.144
  Angle     :  0.577   6.088  17529  Z= 0.308
  Chirality :  0.048   0.260   1986
  Planarity :  0.003   0.050   2268
  Dihedral  :  4.653  18.859   1812
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.87 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 16.08 %
    Favored  : 78.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.19), residues: 1680
  helix:  0.80 (0.64), residues: 81
  sheet: -0.38 (0.21), residues: 600
  loop : -2.33 (0.17), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  80 
 TYR   0.021   0.001   TYR B 176 
 PHE   0.012   0.001   PHE A 322 
 TRP   0.017   0.001   TRP A 237 
 HIS   0.006   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12888)
  covalent geometry    : angle       0.57654 (17529)
  hydrogen bonds       : bond        0.03150 (  210)
  hydrogen bonds       : angle       4.86531 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 133
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9169 (p) cc_final: 0.8854 (m)
REVERT: A  232 MET cc_start: 0.8664 (mmt) cc_final: 0.8420 (mmt)
REVERT: B  180 SER cc_start: 0.9287 (p) cc_final: 0.8905 (m)
REVERT: B  232 MET cc_start: 0.8798 (mmt) cc_final: 0.8089 (mmt)
REVERT: B  328 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8307 (mm-40)
REVERT: C   28 PHE cc_start: 0.8501 (t80) cc_final: 0.8232 (t80)
REVERT: C   83 ASP cc_start: 0.7838 (t0) cc_final: 0.7552 (t0)
REVERT: C  180 SER cc_start: 0.9220 (p) cc_final: 0.8952 (m)
REVERT: C  232 MET cc_start: 0.8333 (mmt) cc_final: 0.8019 (mmt)
REVERT: C  268 ILE cc_start: 0.9074 (tp) cc_final: 0.8841 (tp)
REVERT: C  508 GLN cc_start: 0.8404 (tp40) cc_final: 0.8165 (tp40)
REVERT: C  575 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8256 (tp)
  outliers start: 73
  outliers final: 52
  residues processed: 192
  average time/residue: 0.0736
  time to fit residues: 23.7543
Evaluate side-chains
  180 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 127
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 161 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 149 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 163 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 162 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN
** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 ASN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 GLN
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 566 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.101991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.082755 restraints weight = 19593.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.084725 restraints weight = 14016.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.085436 restraints weight = 10166.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.085739 restraints weight = 8701.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.085912 restraints weight = 8336.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  12888  Z= 0.259
  Angle     :  0.670   6.257  17529  Z= 0.362
  Chirality :  0.052   0.265   1986
  Planarity :  0.003   0.045   2268
  Dihedral  :  5.215  19.861   1812
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.54 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 15.50 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.19), residues: 1680
  helix:  0.57 (0.64), residues: 81
  sheet: -0.54 (0.22), residues: 576
  loop : -2.50 (0.16), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 238 
 TYR   0.023   0.002   TYR B 176 
 PHE   0.015   0.002   PHE A 322 
 TRP   0.026   0.002   TRP B 237 
 HIS   0.008   0.002   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 (12888)
  covalent geometry    : angle       0.67000 (17529)
  hydrogen bonds       : bond        0.04190 (  210)
  hydrogen bonds       : angle       5.38215 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 129
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9225 (p) cc_final: 0.8971 (m)
REVERT: A  232 MET cc_start: 0.8612 (mmt) cc_final: 0.8410 (mmt)
REVERT: A  508 GLN cc_start: 0.8719 (tp40) cc_final: 0.8470 (tp40)
REVERT: B   43 TRP cc_start: 0.9174 (t60) cc_final: 0.8835 (t60)
REVERT: B  180 SER cc_start: 0.9312 (p) cc_final: 0.8910 (m)
REVERT: B  232 MET cc_start: 0.8803 (mmt) cc_final: 0.8185 (mmt)
REVERT: B  293 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8413 (mtp)
REVERT: C   25 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8464 (ttm)
REVERT: C   83 ASP cc_start: 0.7805 (t0) cc_final: 0.7523 (t0)
REVERT: C  189 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7398 (m-10)
REVERT: C  232 MET cc_start: 0.8525 (mmt) cc_final: 0.8165 (mmt)
REVERT: C  253 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.8872 (m-40)
REVERT: C  508 GLN cc_start: 0.8597 (tp40) cc_final: 0.8396 (tp40)
  outliers start: 82
  outliers final: 65
  residues processed: 187
  average time/residue: 0.0809
  time to fit residues: 24.6713
Evaluate side-chains
  187 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 118
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  235 ASN
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  414 ASN
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   74 ASP
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  235 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  370 ASN
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain B residue  575 ILE
Chi-restraints excluded: chain C residue   25 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   74 ASP
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  414 ASN
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 149 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 566 GLN
C 118 GLN
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 566 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.104331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.085964 restraints weight = 19364.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.086060 restraints weight = 15833.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.086558 restraints weight = 17589.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.087097 restraints weight = 13514.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.088463 restraints weight = 12060.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12888  Z= 0.136
  Angle     :  0.590   6.278  17529  Z= 0.315
  Chirality :  0.048   0.260   1986
  Planarity :  0.003   0.040   2268
  Dihedral  :  4.827  19.491   1812
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.93 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 17.54 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.19), residues: 1680
  helix:  0.74 (0.64), residues: 81
  sheet: -0.44 (0.22), residues: 603
  loop : -2.42 (0.17), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  80 
 TYR   0.015   0.001   TYR B 176 
 PHE   0.013   0.001   PHE B 322 
 TRP   0.019   0.001   TRP A 237 
 HIS   0.007   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12888)
  covalent geometry    : angle       0.58993 (17529)
  hydrogen bonds       : bond        0.03003 (  210)
  hydrogen bonds       : angle       4.94019 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 129
  time to evaluate  : 0.466 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9198 (p) cc_final: 0.8862 (m)
REVERT: A  238 ARG cc_start: 0.8010 (ptm160) cc_final: 0.7681 (mtp-110)
REVERT: A  575 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7748 (tp)
REVERT: B  155 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7888 (mm-30)
REVERT: B  180 SER cc_start: 0.9353 (p) cc_final: 0.8941 (m)
REVERT: B  232 MET cc_start: 0.8739 (mmt) cc_final: 0.8192 (mmt)
REVERT: B  253 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8747 (m-40)
REVERT: C   83 ASP cc_start: 0.7900 (t0) cc_final: 0.7640 (t0)
REVERT: C  508 GLN cc_start: 0.8516 (tp40) cc_final: 0.8294 (tp40)
  outliers start: 72
  outliers final: 60
  residues processed: 183
  average time/residue: 0.0834
  time to fit residues: 24.3272
Evaluate side-chains
  189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 127
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  237 TRP
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  253 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  414 ASN
Chi-restraints excluded: chain C residue  429 THR
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Chi-restraints excluded: chain C residue  575 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 155 optimal weight:    8.9990
   chunk 149 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 131 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 137 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.100869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.081531 restraints weight = 19448.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.082550 restraints weight = 13955.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.083610 restraints weight = 12976.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.084261 restraints weight = 10050.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.084345 restraints weight = 9572.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12888  Z= 0.228
  Angle     :  0.646   6.165  17529  Z= 0.347
  Chirality :  0.050   0.261   1986
  Planarity :  0.003   0.036   2268
  Dihedral  :  5.074  20.103   1812
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.83 %
    Favored  : 89.11 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 17.40 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.19), residues: 1680
  helix:  0.59 (0.63), residues: 81
  sheet: -0.46 (0.22), residues: 600
  loop : -2.52 (0.17), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  80 
 TYR   0.019   0.002   TYR B 176 
 PHE   0.017   0.002   PHE A 276 
 TRP   0.023   0.002   TRP A 237 
 HIS   0.007   0.002   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (12888)
  covalent geometry    : angle       0.64589 (17529)
  hydrogen bonds       : bond        0.03827 (  210)
  hydrogen bonds       : angle       5.17911 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 121
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9255 (p) cc_final: 0.8982 (m)
REVERT: A  232 MET cc_start: 0.8682 (mmt) cc_final: 0.8359 (mmt)
REVERT: A  575 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7917 (tp)
REVERT: B   43 TRP cc_start: 0.9145 (t60) cc_final: 0.8807 (t60)
REVERT: B  155 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7831 (mm-30)
REVERT: B  180 SER cc_start: 0.9327 (p) cc_final: 0.8903 (m)
REVERT: B  232 MET cc_start: 0.8785 (mmt) cc_final: 0.8170 (mmt)
REVERT: B  253 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8868 (m-40)
REVERT: C   25 MET cc_start: 0.8731 (ttm) cc_final: 0.8449 (ttm)
REVERT: C   83 ASP cc_start: 0.7864 (t0) cc_final: 0.7579 (t0)
REVERT: C  189 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7478 (m-10)
REVERT: C  232 MET cc_start: 0.8590 (mmt) cc_final: 0.8216 (mmt)
REVERT: C  253 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.8875 (m-40)
REVERT: C  508 GLN cc_start: 0.8548 (tp40) cc_final: 0.8339 (tp40)
  outliers start: 81
  outliers final: 68
  residues processed: 183
  average time/residue: 0.0824
  time to fit residues: 24.7104
Evaluate side-chains
  189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 117
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  237 TRP
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  253 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  237 TRP
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  343 ILE
Chi-restraints excluded: chain C residue  414 ASN
Chi-restraints excluded: chain C residue  429 THR
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 163 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 151 optimal weight:    1.9990
   chunk 123 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 96 optimal weight:    0.2980
   chunk 35 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.102374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.084446 restraints weight = 19397.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.084863 restraints weight = 15410.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.086312 restraints weight = 15364.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.086764 restraints weight = 11354.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.086918 restraints weight = 10750.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12888  Z= 0.189
  Angle     :  0.622   6.290  17529  Z= 0.333
  Chirality :  0.049   0.259   1986
  Planarity :  0.003   0.036   2268
  Dihedral  :  5.004  18.885   1812
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.64 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 17.76 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.19), residues: 1680
  helix:  0.62 (0.63), residues: 81
  sheet: -0.57 (0.22), residues: 615
  loop : -2.48 (0.17), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 238 
 TYR   0.016   0.001   TYR B 176 
 PHE   0.016   0.002   PHE A 322 
 TRP   0.022   0.002   TRP A 237 
 HIS   0.007   0.002   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (12888)
  covalent geometry    : angle       0.62189 (17529)
  hydrogen bonds       : bond        0.03463 (  210)
  hydrogen bonds       : angle       5.12232 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 120
  time to evaluate  : 0.473 
Fit side-chains
REVERT: A  180 SER cc_start: 0.9268 (p) cc_final: 0.8981 (m)
REVERT: A  232 MET cc_start: 0.8665 (mmt) cc_final: 0.8317 (mmt)
REVERT: A  274 CYS cc_start: 0.8575 (t) cc_final: 0.8228 (t)
REVERT: A  491 MET cc_start: 0.8381 (mmm) cc_final: 0.8133 (tpp)
REVERT: A  575 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7834 (tp)
REVERT: B   43 TRP cc_start: 0.9127 (t60) cc_final: 0.8793 (t60)
REVERT: B  155 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7845 (mm-30)
REVERT: B  180 SER cc_start: 0.9337 (p) cc_final: 0.8910 (m)
REVERT: B  232 MET cc_start: 0.8768 (mmt) cc_final: 0.8214 (mmt)
REVERT: B  253 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8822 (m-40)
REVERT: C   83 ASP cc_start: 0.7953 (t0) cc_final: 0.7685 (t0)
REVERT: C  508 GLN cc_start: 0.8606 (tp40) cc_final: 0.8400 (tp40)
  outliers start: 81
  outliers final: 73
  residues processed: 185
  average time/residue: 0.0814
  time to fit residues: 24.6201
Evaluate side-chains
  190 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 115
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 SER
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  237 TRP
Chi-restraints excluded: chain A residue  253 ASN
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  154 THR
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  253 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 SER
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  180 SER
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  237 TRP
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  414 ASN
Chi-restraints excluded: chain C residue  429 THR
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Chi-restraints excluded: chain C residue  568 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 104 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 158 optimal weight:    7.9990
   chunk 154 optimal weight:    0.0970
   chunk 49 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 126 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN
A 566 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.111782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.091993 restraints weight = 18869.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.094293 restraints weight = 12020.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.095971 restraints weight = 8887.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.097070 restraints weight = 7166.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.097760 restraints weight = 6182.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12888  Z= 0.113
  Angle     :  0.570   8.283  17529  Z= 0.301
  Chirality :  0.047   0.262   1986
  Planarity :  0.003   0.036   2268
  Dihedral  :  4.570  17.242   1812
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.51 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 19.23 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.20), residues: 1680
  helix:  0.82 (0.65), residues: 81
  sheet: -0.49 (0.22), residues: 615
  loop : -2.37 (0.17), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  80 
 TYR   0.010   0.001   TYR C 175 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.014   0.001   TRP A 237 
 HIS   0.006   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12888)
  covalent geometry    : angle       0.57038 (17529)
  hydrogen bonds       : bond        0.02601 (  210)
  hydrogen bonds       : angle       4.70020 (  513)

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

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

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3360 Ramachandran restraints generated.
    1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 131
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  171 THR cc_start: 0.8700 (m) cc_final: 0.8437 (p)
REVERT: A  180 SER cc_start: 0.9145 (p) cc_final: 0.8817 (m)
REVERT: A  232 MET cc_start: 0.8624 (mmt) cc_final: 0.8299 (mmt)
REVERT: A  238 ARG cc_start: 0.7919 (ptm160) cc_final: 0.7599 (mtp-110)
REVERT: A  274 CYS cc_start: 0.8240 (t) cc_final: 0.7902 (t)
REVERT: A  491 MET cc_start: 0.8216 (mmm) cc_final: 0.7896 (tpp)
REVERT: A  575 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7759 (tp)
REVERT: B  143 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8641 (mm)
REVERT: B  155 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7777 (mm-30)
REVERT: B  180 SER cc_start: 0.9220 (p) cc_final: 0.8763 (m)
REVERT: B  253 ASN cc_start: 0.9185 (OUTLIER) cc_final: 0.8973 (m-40)
REVERT: C   83 ASP cc_start: 0.7756 (t0) cc_final: 0.7523 (t0)
REVERT: C  253 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8977 (m-40)
REVERT: C  268 ILE cc_start: 0.9053 (tp) cc_final: 0.8823 (tp)
  outliers start: 64
  outliers final: 57
  residues processed: 182
  average time/residue: 0.0878
  time to fit residues: 25.4508
Evaluate side-chains
  189 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 128
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 MET
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  163 THR
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  300 PHE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  321 ASN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  429 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  467 LEU
Chi-restraints excluded: chain A residue  468 HIS
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   51 SER
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  125 SER
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  253 ASN
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  300 PHE
Chi-restraints excluded: chain B residue  303 ILE
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  320 CYS
Chi-restraints excluded: chain B residue  429 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  492 SER
Chi-restraints excluded: chain B residue  509 ILE
Chi-restraints excluded: chain B residue  565 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   94 LEU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain C residue  125 SER
Chi-restraints excluded: chain C residue  163 THR
Chi-restraints excluded: chain C residue  183 LEU
Chi-restraints excluded: chain C residue  189 PHE
Chi-restraints excluded: chain C residue  199 LEU
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  253 ASN
Chi-restraints excluded: chain C residue  300 PHE
Chi-restraints excluded: chain C residue  303 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  320 CYS
Chi-restraints excluded: chain C residue  414 ASN
Chi-restraints excluded: chain C residue  438 LEU
Chi-restraints excluded: chain C residue  467 LEU
Chi-restraints excluded: chain C residue  468 HIS
Chi-restraints excluded: chain C residue  492 SER
Chi-restraints excluded: chain C residue  509 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 414 ASN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 414 ASN
** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.089553 restraints weight = 19144.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.090353 restraints weight = 15052.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.091205 restraints weight = 11948.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.092040 restraints weight = 10210.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.092130 restraints weight = 8970.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12888  Z= 0.154
  Angle     :  0.595   8.369  17529  Z= 0.316
  Chirality :  0.048   0.261   1986
  Planarity :  0.003   0.036   2268
  Dihedral  :  4.670  17.204   1812
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.23 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 19.37 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.15 (0.20), residues: 1680
  helix:  0.76 (0.64), residues: 81
  sheet: -0.49 (0.22), residues: 618
  loop : -2.37 (0.17), residues: 981

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  80 
 TYR   0.015   0.001   TYR B 176 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.018   0.001   TRP A 237 
 HIS   0.006   0.001   HIS C 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12888)
  covalent geometry    : angle       0.59490 (17529)
  hydrogen bonds       : bond        0.03109 (  210)
  hydrogen bonds       : angle       4.79846 (  513)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1633.02 seconds
wall clock time: 29 minutes 22.31 seconds (1762.31 seconds total)