Starting phenix.real_space_refine
on Wed Mar  4 09:45:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vff_31951/03_2026/7vff_31951.cif"
  }
  resolution = 4.1
  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=   1.000
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      36      5.16       5
     C    8043      2.51       5
     N    2043      2.21       5
     O    2457      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: 12579
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4193
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4193
          Classifications: {'peptide': 527}
          Link IDs: {'PTRANS': 25, 'TRANS': 501}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   ARG A  83 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  83 " occ=0.50
    residue:
      pdb=" N   ARG B  83 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  83 " occ=0.50
    residue:
      pdb=" N   ARG C  83 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG C  83 " occ=0.50
  Time building chain proxies: 3.33, per 1000 atoms: 0.26
  Number of scatterers: 12579
  At special positions: 0
  Unit cell: (99.68, 104.16, 106.4, 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      36     16.00
     O    2457      8.00
     N    2043      7.00
     C    8043      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: 0.86
  Conformation dependent library (CDL) restraints added in 670.4 milliseconds
  

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 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:
      42 helices and 33 sheets defined
      20.3% alpha, 43.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 94
    Processing helix  chain 'A' and resid 112 through 120
    Processing helix  chain 'A' and resid 122 through 129
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.696A  pdb=" N   VAL A 164 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 170
    Processing helix  chain 'A' and resid 186 through 189
    Processing helix  chain 'A' and resid 198 through 206
    Processing helix  chain 'A' and resid 279 through 295
      removed outlier: 4.169A  pdb=" N   ASP A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ASP A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 396 through 401
      removed outlier: 3.865A  pdb=" N   TRP A 400 " --> pdb=" O   PRO A 396 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR A 401 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 396 through 401'
    Processing helix  chain 'A' and resid 413 through 418
    Processing helix  chain 'A' and resid 458 through 469
    Processing helix  chain 'A' and resid 516 through 521
    Processing helix  chain 'B' and resid 89 through 94
    Processing helix  chain 'B' and resid 112 through 120
    Processing helix  chain 'B' and resid 122 through 129
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 3.696A  pdb=" N   VAL B 164 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 170
    Processing helix  chain 'B' and resid 186 through 189
    Processing helix  chain 'B' and resid 198 through 206
    Processing helix  chain 'B' and resid 279 through 295
      removed outlier: 4.170A  pdb=" N   ASP B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ASP B 294 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 396 through 401
      removed outlier: 3.865A  pdb=" N   TRP B 400 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   THR B 401 " --> pdb=" O   VAL B 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 396 through 401'
    Processing helix  chain 'B' and resid 413 through 418
    Processing helix  chain 'B' and resid 458 through 469
    Processing helix  chain 'B' and resid 516 through 521
    Processing helix  chain 'C' and resid 89 through 94
    Processing helix  chain 'C' and resid 112 through 120
    Processing helix  chain 'C' and resid 122 through 129
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 160 through 164
      removed outlier: 3.696A  pdb=" N   VAL C 164 " --> pdb=" O   PRO C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 170
    Processing helix  chain 'C' and resid 186 through 189
    Processing helix  chain 'C' and resid 198 through 206
    Processing helix  chain 'C' and resid 279 through 295
      removed outlier: 4.169A  pdb=" N   ASP C 293 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   ASP C 294 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 389 through 395
    Processing helix  chain 'C' and resid 396 through 401
      removed outlier: 3.866A  pdb=" N   TRP C 400 " --> pdb=" O   PRO C 396 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   THR C 401 " --> pdb=" O   VAL C 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 396 through 401'
    Processing helix  chain 'C' and resid 413 through 418
    Processing helix  chain 'C' and resid 458 through 469
    Processing helix  chain 'C' and resid 516 through 521
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40
      removed outlier: 3.951A  pdb=" N   ILE A 215 " --> pdb=" O   HIS A  68 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS A  68 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU A  66 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A  69 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40
      removed outlier: 3.951A  pdb=" N   ILE A 215 " --> pdb=" O   HIS A  68 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS A  68 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU A  66 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44
      removed outlier: 7.157A  pdb=" N   ASN A  96 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   GLU A 111 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL A  98 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   GLU A 109 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE A 100 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79
      removed outlier: 6.941A  pdb=" N   VAL A  78 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141
      removed outlier: 5.729A  pdb=" N   ARG A  83 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236
      removed outlier: 4.473A  pdb=" N   GLN A 522 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER A 254 " --> pdb=" O   ASN A 530 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU A 532 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA A 252 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 252 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478
      removed outlier: 3.857A  pdb=" N   ARG A 475 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA A 252 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU A 532 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER A 254 " --> pdb=" O   ASN A 530 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLN A 522 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 247
      removed outlier: 6.318A  pdb=" N   LYS A 502 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   SER A 504 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   VAL A 445 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG A 506 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LEU A 443 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL A 508 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   PHE A 447 " --> pdb=" O   VAL A 451 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL A 451 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 299
    Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323
      removed outlier: 6.760A  pdb=" N   ASP A 327 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE A 368 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   TYR A 329 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLY A 370 " --> pdb=" O   TYR A 329 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS A 331 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   TYR A 372 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ASP A 333 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE A 365 " --> pdb=" O   HIS A 386 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   HIS A 386 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ALA A 367 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ILE A 384 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR A 369 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG A 378 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 349 through 350
    Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 40
      removed outlier: 3.951A  pdb=" N   ILE B 215 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   HIS B  68 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   LEU B  66 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU B  69 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40
      removed outlier: 3.951A  pdb=" N   ILE B 215 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   HIS B  68 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   LEU B  66 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 44
      removed outlier: 7.157A  pdb=" N   ASN B  96 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   GLU B 111 " --> pdb=" O   ASN B  96 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B  98 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   GLU B 109 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE B 100 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 79
      removed outlier: 6.942A  pdb=" N   VAL B  78 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 141
      removed outlier: 5.729A  pdb=" N   ARG B  83 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 236
      removed outlier: 4.473A  pdb=" N   GLN B 522 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER B 254 " --> pdb=" O   ASN B 530 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU B 532 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA B 252 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 478
      removed outlier: 3.857A  pdb=" N   ARG B 475 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU B 532 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER B 254 " --> pdb=" O   ASN B 530 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLN B 522 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 247
      removed outlier: 6.317A  pdb=" N   LYS B 502 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   PHE B 447 " --> pdb=" O   LYS B 502 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   SER B 504 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   ARG B 506 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   LEU B 443 " --> pdb=" O   ARG B 506 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   VAL B 508 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   PHE B 447 " --> pdb=" O   VAL B 451 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL B 451 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 296 through 299
    Processing sheet with id=AC3, first strand: chain 'B' and resid 320 through 323
      removed outlier: 6.760A  pdb=" N   ASP B 327 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE B 368 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   TYR B 329 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLY B 370 " --> pdb=" O   TYR B 329 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LYS B 331 " --> pdb=" O   GLY B 370 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   TYR B 372 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ASP B 333 " --> pdb=" O   TYR B 372 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE B 365 " --> pdb=" O   HIS B 386 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   HIS B 386 " --> pdb=" O   PHE B 365 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ALA B 367 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ILE B 384 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   THR B 369 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B 378 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 349 through 350
    Processing sheet with id=AC5, first strand: chain 'C' and resid 32 through 40
      removed outlier: 3.952A  pdb=" N   ILE C 215 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU C  66 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU C  69 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 32 through 40
      removed outlier: 3.952A  pdb=" N   ILE C 215 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   LEU C  66 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 42 through 44
      removed outlier: 7.158A  pdb=" N   ASN C  96 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   GLU C 111 " --> pdb=" O   ASN C  96 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL C  98 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   GLU C 109 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE C 100 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 78 through 79
      removed outlier: 6.941A  pdb=" N   VAL C  78 " --> pdb=" O   ILE C 148 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 139 through 141
      removed outlier: 5.729A  pdb=" N   ARG C  83 " --> pdb=" O   ASP C 194 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 227 through 236
      removed outlier: 4.473A  pdb=" N   GLN C 522 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER C 254 " --> pdb=" O   ASN C 530 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU C 532 " --> pdb=" O   ALA C 252 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA C 252 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA C 252 " --> pdb=" O   ILE C 492 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 475 through 478
      removed outlier: 3.857A  pdb=" N   ARG C 475 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   ALA C 252 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LEU C 532 " --> pdb=" O   ALA C 252 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   SER C 254 " --> pdb=" O   ASN C 530 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLN C 522 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 243 through 247
      removed outlier: 6.318A  pdb=" N   LYS C 502 " --> pdb=" O   PHE C 447 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   PHE C 447 " --> pdb=" O   LYS C 502 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   SER C 504 " --> pdb=" O   VAL C 445 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   VAL C 445 " --> pdb=" O   SER C 504 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ARG C 506 " --> pdb=" O   LEU C 443 " (cutoff:3.500A)
      removed outlier: 4.685A  pdb=" N   LEU C 443 " --> pdb=" O   ARG C 506 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   VAL C 508 " --> pdb=" O   SER C 441 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   PHE C 447 " --> pdb=" O   VAL C 451 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL C 451 " --> pdb=" O   PHE C 447 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 299
    Processing sheet with id=AD5, first strand: chain 'C' and resid 320 through 323
      removed outlier: 6.760A  pdb=" N   ASP C 327 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   ILE C 368 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   TYR C 329 " --> pdb=" O   ILE C 368 " (cutoff:3.500A)
      removed outlier: 8.092A  pdb=" N   GLY C 370 " --> pdb=" O   TYR C 329 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS C 331 " --> pdb=" O   GLY C 370 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   TYR C 372 " --> pdb=" O   LYS C 331 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASP C 333 " --> pdb=" O   TYR C 372 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   HIS C 383 " --> pdb=" O   THR C 369 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   THR C 371 " --> pdb=" O   PHE C 381 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   PHE C 381 " --> pdb=" O   THR C 371 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   SER C 373 " --> pdb=" O   THR C 379 " (cutoff:3.500A)
      removed outlier: 5.900A  pdb=" N   THR C 379 " --> pdb=" O   SER C 373 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 349 through 350

    515 hydrogen bonds defined for protein.
    1365 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: 2.59

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3989
        1.34 -     1.45: 1878
        1.45 -     1.57: 6928
        1.57 -     1.69: 0
        1.69 -     1.80: 60
  Bond restraints: 12855
  Sorted by residual:
  bond pdb=" N   TYR C 453 "
       pdb=" CA  TYR C 453 "
    ideal  model  delta    sigma   weight residual
    1.455  1.483 -0.028 1.18e-02 7.18e+03 5.51e+00
  bond pdb=" N   TYR A 453 "
       pdb=" CA  TYR A 453 "
    ideal  model  delta    sigma   weight residual
    1.455  1.483 -0.028 1.18e-02 7.18e+03 5.46e+00
  bond pdb=" N   TYR B 453 "
       pdb=" CA  TYR B 453 "
    ideal  model  delta    sigma   weight residual
    1.455  1.483 -0.027 1.18e-02 7.18e+03 5.39e+00
  bond pdb=" N   TYR C 359 "
       pdb=" CA  TYR C 359 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.23e-02 6.61e+03 4.04e+00
  bond pdb=" N   TYR A 359 "
       pdb=" CA  TYR A 359 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.23e-02 6.61e+03 4.00e+00
  ... (remaining 12850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 16810
        1.69 -     3.38: 632
        3.38 -     5.07: 39
        5.07 -     6.76: 6
        6.76 -     8.45: 3
  Bond angle restraints: 17490
  Sorted by residual:
  angle pdb=" CA  ASP A 333 "
        pdb=" C   ASP A 333 "
        pdb=" O   ASP A 333 "
      ideal   model   delta    sigma   weight residual
     121.72  117.99    3.73 1.18e+00 7.18e-01 9.98e+00
  angle pdb=" CA  ASP B 333 "
        pdb=" C   ASP B 333 "
        pdb=" O   ASP B 333 "
      ideal   model   delta    sigma   weight residual
     121.72  118.02    3.70 1.18e+00 7.18e-01 9.84e+00
  angle pdb=" CA  ASP C 333 "
        pdb=" C   ASP C 333 "
        pdb=" O   ASP C 333 "
      ideal   model   delta    sigma   weight residual
     121.72  118.03    3.69 1.18e+00 7.18e-01 9.76e+00
  angle pdb=" CA  TYR C 359 "
        pdb=" C   TYR C 359 "
        pdb=" O   TYR C 359 "
      ideal   model   delta    sigma   weight residual
     120.58  117.66    2.92 1.07e+00 8.73e-01 7.46e+00
  angle pdb=" CA  TYR B 359 "
        pdb=" C   TYR B 359 "
        pdb=" O   TYR B 359 "
      ideal   model   delta    sigma   weight residual
     120.58  117.66    2.92 1.07e+00 8.73e-01 7.45e+00
  ... (remaining 17485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 6994
       17.48 -    34.96: 600
       34.96 -    52.45: 86
       52.45 -    69.93: 15
       69.93 -    87.41: 24
  Dihedral angle restraints: 7719
    sinusoidal: 3036
      harmonic: 4683
  Sorted by residual:
  dihedral pdb=" CA  PRO A 483 "
           pdb=" C   PRO A 483 "
           pdb=" N   LYS A 484 "
           pdb=" CA  LYS A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.61  -21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  PRO B 483 "
           pdb=" C   PRO B 483 "
           pdb=" N   LYS B 484 "
           pdb=" CA  LYS B 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.61  -21.39     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  PRO C 483 "
           pdb=" C   PRO C 483 "
           pdb=" N   LYS C 484 "
           pdb=" CA  LYS C 484 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.65  -21.35     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 7716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1262
       0.044 -    0.088: 504
       0.088 -    0.132: 232
       0.132 -    0.176: 12
       0.176 -    0.220: 6
  Chirality restraints: 2016
  Sorted by residual:
  chirality pdb=" CA  TYR C 359 "
            pdb=" N   TYR C 359 "
            pdb=" C   TYR C 359 "
            pdb=" CB  TYR C 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR A 359 "
            pdb=" N   TYR A 359 "
            pdb=" C   TYR A 359 "
            pdb=" CB  TYR A 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR B 359 "
            pdb=" N   TYR B 359 "
            pdb=" C   TYR B 359 "
            pdb=" CB  TYR B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 2013 not shown)

  Planarity restraints: 2235
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 209 "   -0.035 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO B 210 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 210 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 210 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 209 "    0.035 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO A 210 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 209 "    0.034 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO C 210 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO C 210 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 210 "    0.029 5.00e-02 4.00e+02
  ... (remaining 2232 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 4280
        2.85 -     3.36: 10495
        3.36 -     3.87: 20247
        3.87 -     4.39: 22484
        4.39 -     4.90: 39944
  Nonbonded interactions: 97450
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 322 "
            pdb=" OD1 ASP C 327 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG  SER B 322 "
            pdb=" OD1 ASP B 327 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG  SER A 322 "
            pdb=" OD1 ASP A 327 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   PHE B  22 "
            pdb=" NZ  LYS C 172 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" NE2 HIS A 128 "
            pdb=" OE1 GLU B 465 "
     model   vdw
     2.390 3.120
  ... (remaining 97445 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=0.50 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:             1.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.870
  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:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
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      :  0.007   0.064  12855  Z= 0.307
  Angle     :  0.723   8.446  17490  Z= 0.411
  Chirality :  0.054   0.220   2016
  Planarity :  0.005   0.052   2235
  Dihedral  : 13.866  87.411   4707
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  4.95 %
    Favored  : 94.64 %
  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: -0.82 (0.19), residues: 1569
  helix: -1.03 (0.29), residues: 237
  sheet:  0.06 (0.22), residues: 462
  loop : -0.67 (0.19), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG B 193 
 TYR   0.023   0.002   TYR C 157 
 PHE   0.028   0.003   PHE B 479 
 TRP   0.014   0.003   TRP C 108 
 HIS   0.004   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00715 (12855)
  covalent geometry    : angle       0.72338 (17490)
  hydrogen bonds       : bond        0.21763 (  455)
  hydrogen bonds       : angle       7.38313 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  431 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 425
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8844 (tttt) cc_final: 0.8586 (tttp)
REVERT: A  208 TYR cc_start: 0.8073 (m-80) cc_final: 0.7810 (m-80)
REVERT: A  298 VAL cc_start: 0.8694 (t) cc_final: 0.8002 (m)
REVERT: A  380 ILE cc_start: 0.8680 (mm) cc_final: 0.8341 (mt)
REVERT: A  392 ASP cc_start: 0.6550 (m-30) cc_final: 0.6300 (m-30)
REVERT: A  432 ASP cc_start: 0.8378 (p0) cc_final: 0.8002 (p0)
REVERT: A  437 THR cc_start: 0.8048 (m) cc_final: 0.7679 (p)
REVERT: A  531 ASP cc_start: 0.6988 (m-30) cc_final: 0.6754 (m-30)
REVERT: A  546 ILE cc_start: 0.9068 (mm) cc_final: 0.8825 (tt)
REVERT: B  163 ASP cc_start: 0.8358 (m-30) cc_final: 0.8024 (m-30)
REVERT: B  173 LEU cc_start: 0.8731 (mp) cc_final: 0.8283 (mt)
REVERT: B  178 ILE cc_start: 0.9373 (mm) cc_final: 0.9149 (mm)
REVERT: B  208 TYR cc_start: 0.8119 (m-80) cc_final: 0.7888 (m-80)
REVERT: B  253 THR cc_start: 0.8777 (p) cc_final: 0.8465 (m)
REVERT: B  298 VAL cc_start: 0.8366 (t) cc_final: 0.7621 (m)
REVERT: B  380 ILE cc_start: 0.8509 (mm) cc_final: 0.8256 (mt)
REVERT: B  392 ASP cc_start: 0.6210 (m-30) cc_final: 0.5901 (m-30)
REVERT: C   73 LEU cc_start: 0.8979 (mt) cc_final: 0.8736 (mt)
REVERT: C  179 THR cc_start: 0.8959 (m) cc_final: 0.8712 (p)
REVERT: C  266 THR cc_start: 0.8078 (p) cc_final: 0.7791 (t)
REVERT: C  298 VAL cc_start: 0.8522 (t) cc_final: 0.7705 (m)
REVERT: C  380 ILE cc_start: 0.8634 (mm) cc_final: 0.8343 (mt)
REVERT: C  392 ASP cc_start: 0.6393 (m-30) cc_final: 0.5765 (m-30)
REVERT: C  425 ASP cc_start: 0.8194 (t70) cc_final: 0.7919 (t0)
REVERT: C  432 ASP cc_start: 0.8161 (p0) cc_final: 0.7732 (p0)
REVERT: C  455 GLU cc_start: 0.7334 (pt0) cc_final: 0.7070 (pt0)
REVERT: C  493 THR cc_start: 0.8541 (p) cc_final: 0.8309 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 428
  average time/residue: 0.1175
  time to fit residues: 71.4945
Evaluate side-chains
  221 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 218
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0870
   chunk 149 optimal weight:    4.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
A 278 GLN
A 480 ASN
B  97 HIS
C  97 HIS
C 128 HIS
C 480 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.090887 restraints weight = 22389.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.094223 restraints weight = 12702.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.096480 restraints weight = 8615.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.098025 restraints weight = 6596.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.099059 restraints weight = 5492.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12855  Z= 0.136
  Angle     :  0.534  10.124  17490  Z= 0.291
  Chirality :  0.049   0.157   2016
  Planarity :  0.004   0.030   2235
  Dihedral  :  4.643  18.906   1725
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  1.78 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.86 %
    Favored  : 97.94 %
  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: -0.07 (0.20), residues: 1569
  helix: -0.11 (0.34), residues: 234
  sheet:  0.38 (0.23), residues: 474
  loop : -0.18 (0.20), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  83 
 TYR   0.017   0.001   TYR C 208 
 PHE   0.015   0.001   PHE A 228 
 TRP   0.011   0.001   TRP B 108 
 HIS   0.003   0.001   HIS C 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12855)
  covalent geometry    : angle       0.53449 (17490)
  hydrogen bonds       : bond        0.04266 (  455)
  hydrogen bonds       : angle       5.63072 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 292
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8821 (tttt) cc_final: 0.8566 (tttp)
REVERT: A  163 ASP cc_start: 0.8509 (m-30) cc_final: 0.8068 (m-30)
REVERT: A  194 ASP cc_start: 0.8718 (p0) cc_final: 0.8305 (p0)
REVERT: A  208 TYR cc_start: 0.8621 (m-80) cc_final: 0.8261 (m-80)
REVERT: A  287 TYR cc_start: 0.9074 (t80) cc_final: 0.8666 (t80)
REVERT: A  298 VAL cc_start: 0.8714 (t) cc_final: 0.8319 (m)
REVERT: A  380 ILE cc_start: 0.8670 (mm) cc_final: 0.8315 (mt)
REVERT: A  546 ILE cc_start: 0.9221 (mm) cc_final: 0.8934 (tt)
REVERT: B  208 TYR cc_start: 0.8837 (m-80) cc_final: 0.8496 (m-80)
REVERT: B  290 ARG cc_start: 0.9002 (mmm160) cc_final: 0.8550 (mmm-85)
REVERT: B  380 ILE cc_start: 0.8782 (mm) cc_final: 0.8454 (mt)
REVERT: B  423 ILE cc_start: 0.9162 (mt) cc_final: 0.8922 (mt)
REVERT: B  424 ASN cc_start: 0.8331 (m-40) cc_final: 0.8047 (t0)
REVERT: B  460 SER cc_start: 0.9030 (p) cc_final: 0.8748 (p)
REVERT: C   73 LEU cc_start: 0.8952 (mt) cc_final: 0.8673 (mt)
REVERT: C   81 MET cc_start: 0.8102 (mtp) cc_final: 0.7703 (mtp)
REVERT: C  179 THR cc_start: 0.8846 (m) cc_final: 0.8303 (p)
REVERT: C  194 ASP cc_start: 0.8511 (p0) cc_final: 0.8027 (p0)
REVERT: C  218 MET cc_start: 0.7761 (mpp) cc_final: 0.7430 (mpp)
REVERT: C  290 ARG cc_start: 0.9068 (mmm160) cc_final: 0.8468 (tpp80)
REVERT: C  298 VAL cc_start: 0.8672 (t) cc_final: 0.8234 (m)
REVERT: C  380 ILE cc_start: 0.8963 (mm) cc_final: 0.8696 (mt)
REVERT: C  383 HIS cc_start: 0.8340 (t-90) cc_final: 0.8103 (t-170)
REVERT: C  423 ILE cc_start: 0.9142 (mt) cc_final: 0.8934 (mt)
REVERT: C  424 ASN cc_start: 0.8426 (m-40) cc_final: 0.8173 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 293
  average time/residue: 0.0984
  time to fit residues: 43.3665
Evaluate side-chains
  205 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 143 optimal weight:    0.2980
   chunk 130 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.113766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.091724 restraints weight = 22960.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.094964 restraints weight = 12928.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.097159 restraints weight = 8841.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.098530 restraints weight = 6828.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.099554 restraints weight = 5760.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12855  Z= 0.107
  Angle     :  0.480   9.019  17490  Z= 0.259
  Chirality :  0.047   0.149   2016
  Planarity :  0.003   0.028   2235
  Dihedral  :  4.257  15.931   1725
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  1.98 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  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:  0.19 (0.21), residues: 1569
  helix:  0.04 (0.34), residues: 237
  sheet:  0.46 (0.23), residues: 477
  loop :  0.08 (0.21), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  83 
 TYR   0.018   0.001   TYR C 208 
 PHE   0.015   0.001   PHE C 199 
 TRP   0.006   0.001   TRP B 108 
 HIS   0.003   0.000   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (12855)
  covalent geometry    : angle       0.47968 (17490)
  hydrogen bonds       : bond        0.03579 (  455)
  hydrogen bonds       : angle       5.16207 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7395 (mp0) cc_final: 0.7139 (pm20)
REVERT: A  126 LEU cc_start: 0.8880 (mp) cc_final: 0.8565 (mp)
REVERT: A  194 ASP cc_start: 0.8465 (p0) cc_final: 0.8025 (p0)
REVERT: A  208 TYR cc_start: 0.8578 (m-80) cc_final: 0.8185 (m-80)
REVERT: A  287 TYR cc_start: 0.9031 (t80) cc_final: 0.8197 (t80)
REVERT: A  357 PHE cc_start: 0.6622 (t80) cc_final: 0.6420 (t80)
REVERT: A  380 ILE cc_start: 0.8632 (mm) cc_final: 0.8320 (mt)
REVERT: A  436 LYS cc_start: 0.8654 (tptp) cc_final: 0.8351 (tppp)
REVERT: A  546 ILE cc_start: 0.9206 (mm) cc_final: 0.8964 (tt)
REVERT: B  166 ASP cc_start: 0.7900 (p0) cc_final: 0.7647 (p0)
REVERT: B  208 TYR cc_start: 0.8753 (m-80) cc_final: 0.8331 (m-80)
REVERT: B  380 ILE cc_start: 0.8801 (mm) cc_final: 0.8535 (mt)
REVERT: B  424 ASN cc_start: 0.8285 (m-40) cc_final: 0.8027 (t0)
REVERT: C  218 MET cc_start: 0.7835 (mpp) cc_final: 0.7471 (mpp)
REVERT: C  287 TYR cc_start: 0.8853 (t80) cc_final: 0.8430 (t80)
REVERT: C  290 ARG cc_start: 0.9058 (mmm160) cc_final: 0.8425 (tpp80)
REVERT: C  380 ILE cc_start: 0.8959 (mm) cc_final: 0.8693 (mt)
REVERT: C  424 ASN cc_start: 0.8341 (m-40) cc_final: 0.8075 (t0)
REVERT: C  432 ASP cc_start: 0.8361 (p0) cc_final: 0.7929 (p0)
REVERT: C  512 MET cc_start: 0.8536 (mtp) cc_final: 0.8125 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0962
  time to fit residues: 37.2662
Evaluate side-chains
  200 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 139 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
C 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.106501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.084560 restraints weight = 23614.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.087616 restraints weight = 13533.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.089676 restraints weight = 9368.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.091002 restraints weight = 7306.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.091917 restraints weight = 6204.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  12855  Z= 0.269
  Angle     :  0.598   6.918  17490  Z= 0.325
  Chirality :  0.049   0.152   2016
  Planarity :  0.004   0.040   2235
  Dihedral  :  4.618  17.257   1725
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.74 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  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: -0.07 (0.21), residues: 1569
  helix: -0.18 (0.34), residues: 234
  sheet:  0.39 (0.23), residues: 465
  loop : -0.15 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 290 
 TYR   0.020   0.002   TYR A  89 
 PHE   0.018   0.002   PHE C 447 
 TRP   0.010   0.001   TRP C 108 
 HIS   0.004   0.001   HIS C 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (12855)
  covalent geometry    : angle       0.59810 (17490)
  hydrogen bonds       : bond        0.04531 (  455)
  hydrogen bonds       : angle       5.39572 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ASP cc_start: 0.8471 (p0) cc_final: 0.7995 (p0)
REVERT: A  208 TYR cc_start: 0.8767 (m-80) cc_final: 0.8361 (m-10)
REVERT: A  282 ASP cc_start: 0.8733 (m-30) cc_final: 0.8457 (m-30)
REVERT: A  380 ILE cc_start: 0.8749 (mm) cc_final: 0.8516 (mt)
REVERT: A  546 ILE cc_start: 0.9248 (mm) cc_final: 0.8972 (tt)
REVERT: B  166 ASP cc_start: 0.8007 (p0) cc_final: 0.7759 (p0)
REVERT: B  208 TYR cc_start: 0.8804 (m-80) cc_final: 0.8415 (m-80)
REVERT: B  380 ILE cc_start: 0.8807 (mm) cc_final: 0.8557 (mt)
REVERT: B  539 GLN cc_start: 0.8179 (mp10) cc_final: 0.7908 (mp10)
REVERT: C  218 MET cc_start: 0.7902 (mpp) cc_final: 0.7539 (mpp)
REVERT: C  282 ASP cc_start: 0.8642 (m-30) cc_final: 0.8376 (m-30)
REVERT: C  290 ARG cc_start: 0.9106 (mmm160) cc_final: 0.8356 (tpp80)
REVERT: C  380 ILE cc_start: 0.9029 (mm) cc_final: 0.8813 (mt)
REVERT: C  432 ASP cc_start: 0.8404 (p0) cc_final: 0.8052 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.0997
  time to fit residues: 32.5039
Evaluate side-chains
  180 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 124 optimal weight:    0.9980
   chunk 139 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 155 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 127 optimal weight:    0.7980
   chunk 148 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.107129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.085004 restraints weight = 23573.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.088015 restraints weight = 13492.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.090088 restraints weight = 9354.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.091345 restraints weight = 7314.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.092345 restraints weight = 6233.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12855  Z= 0.186
  Angle     :  0.520   7.306  17490  Z= 0.282
  Chirality :  0.048   0.144   2016
  Planarity :  0.004   0.034   2235
  Dihedral  :  4.523  18.283   1725
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.36 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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: -0.09 (0.21), residues: 1569
  helix: -0.05 (0.35), residues: 234
  sheet:  0.43 (0.23), residues: 462
  loop : -0.25 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 446 
 TYR   0.013   0.002   TYR B 131 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.008   0.001   TRP C 108 
 HIS   0.004   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 (12855)
  covalent geometry    : angle       0.51971 (17490)
  hydrogen bonds       : bond        0.03873 (  455)
  hydrogen bonds       : angle       5.19347 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8455 (m-30) cc_final: 0.8075 (m-30)
REVERT: A  208 TYR cc_start: 0.8786 (m-80) cc_final: 0.8469 (m-10)
REVERT: A  218 MET cc_start: 0.7799 (mpp) cc_final: 0.7520 (mpp)
REVERT: A  282 ASP cc_start: 0.8704 (m-30) cc_final: 0.8461 (m-30)
REVERT: A  380 ILE cc_start: 0.8746 (mm) cc_final: 0.8504 (mt)
REVERT: A  432 ASP cc_start: 0.8516 (p0) cc_final: 0.7877 (p0)
REVERT: A  546 ILE cc_start: 0.9238 (mm) cc_final: 0.9020 (tt)
REVERT: B  165 GLU cc_start: 0.8222 (mm-30) cc_final: 0.8013 (tp30)
REVERT: B  380 ILE cc_start: 0.8797 (mm) cc_final: 0.8575 (mt)
REVERT: B  424 ASN cc_start: 0.8326 (m-40) cc_final: 0.8107 (t0)
REVERT: B  436 LYS cc_start: 0.8790 (tptp) cc_final: 0.8440 (tppp)
REVERT: B  539 GLN cc_start: 0.8291 (mp10) cc_final: 0.7955 (mp10)
REVERT: C  218 MET cc_start: 0.7885 (mpp) cc_final: 0.7544 (mpp)
REVERT: C  249 VAL cc_start: 0.9292 (t) cc_final: 0.8597 (p)
REVERT: C  282 ASP cc_start: 0.8649 (m-30) cc_final: 0.8388 (m-30)
REVERT: C  290 ARG cc_start: 0.9109 (mmm160) cc_final: 0.8327 (tpp80)
REVERT: C  380 ILE cc_start: 0.9047 (mm) cc_final: 0.8839 (mt)
REVERT: C  432 ASP cc_start: 0.8383 (p0) cc_final: 0.8009 (p0)
REVERT: C  539 GLN cc_start: 0.8018 (mp10) cc_final: 0.7800 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0972
  time to fit residues: 30.5400
Evaluate side-chains
  174 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 146 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 151 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 71 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
C 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.104942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.083007 restraints weight = 23899.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.085835 restraints weight = 14098.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.087767 restraints weight = 9991.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.088945 restraints weight = 7932.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.089865 restraints weight = 6828.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12855  Z= 0.242
  Angle     :  0.570   5.513  17490  Z= 0.310
  Chirality :  0.049   0.152   2016
  Planarity :  0.004   0.044   2235
  Dihedral  :  4.719  18.490   1725
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.82 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.33 (0.21), residues: 1569
  helix: -0.19 (0.34), residues: 237
  sheet:  0.24 (0.23), residues: 465
  loop : -0.40 (0.21), residues: 867

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 290 
 TYR   0.022   0.002   TYR C  62 
 PHE   0.015   0.002   PHE C 447 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.004   0.001   HIS B 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (12855)
  covalent geometry    : angle       0.56956 (17490)
  hydrogen bonds       : bond        0.04308 (  455)
  hydrogen bonds       : angle       5.35305 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8453 (m-30) cc_final: 0.8064 (m-30)
REVERT: A  165 GLU cc_start: 0.7592 (tp30) cc_final: 0.7326 (tp30)
REVERT: A  218 MET cc_start: 0.7865 (mpp) cc_final: 0.7578 (mpp)
REVERT: A  254 SER cc_start: 0.9241 (t) cc_final: 0.8925 (p)
REVERT: A  432 ASP cc_start: 0.8480 (p0) cc_final: 0.7865 (p0)
REVERT: A  546 ILE cc_start: 0.9258 (mm) cc_final: 0.8990 (tt)
REVERT: B  453 TYR cc_start: 0.8938 (t80) cc_final: 0.8677 (t80)
REVERT: B  539 GLN cc_start: 0.8324 (mp10) cc_final: 0.7970 (mp10)
REVERT: B  547 MET cc_start: 0.7695 (mtp) cc_final: 0.7434 (mtt)
REVERT: C  218 MET cc_start: 0.7934 (mpp) cc_final: 0.7619 (mpp)
REVERT: C  282 ASP cc_start: 0.8656 (m-30) cc_final: 0.8409 (m-30)
REVERT: C  290 ARG cc_start: 0.9151 (mmm160) cc_final: 0.8475 (tpp80)
REVERT: C  500 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6505 (mtmt)
REVERT: C  539 GLN cc_start: 0.8101 (mp10) cc_final: 0.7886 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0992
  time to fit residues: 30.2049
Evaluate side-chains
  168 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 119 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0270
   chunk 20 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.7040

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.108027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.085821 restraints weight = 23421.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.088882 restraints weight = 13431.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.090946 restraints weight = 9300.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.092316 restraints weight = 7268.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.093204 restraints weight = 6153.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12855  Z= 0.107
  Angle     :  0.478   5.326  17490  Z= 0.259
  Chirality :  0.047   0.145   2016
  Planarity :  0.004   0.035   2235
  Dihedral  :  4.383  17.197   1725
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.36 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.21), residues: 1569
  helix:  0.10 (0.36), residues: 237
  sheet:  0.44 (0.23), residues: 462
  loop : -0.27 (0.22), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 442 
 TYR   0.014   0.001   TYR A 287 
 PHE   0.012   0.001   PHE B 199 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.002   0.001   HIS C 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12855)
  covalent geometry    : angle       0.47756 (17490)
  hydrogen bonds       : bond        0.03339 (  455)
  hydrogen bonds       : angle       5.02282 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8339 (m-30) cc_final: 0.7998 (m-30)
REVERT: A  218 MET cc_start: 0.7822 (mpp) cc_final: 0.7558 (mpp)
REVERT: A  282 ASP cc_start: 0.8695 (m-30) cc_final: 0.8477 (m-30)
REVERT: A  432 ASP cc_start: 0.8434 (p0) cc_final: 0.7817 (p0)
REVERT: B  424 ASN cc_start: 0.8263 (m-40) cc_final: 0.7947 (t0)
REVERT: B  539 GLN cc_start: 0.8230 (mp10) cc_final: 0.7772 (mp10)
REVERT: C  218 MET cc_start: 0.7908 (mpp) cc_final: 0.7570 (mpp)
REVERT: C  282 ASP cc_start: 0.8607 (m-30) cc_final: 0.8389 (m-30)
REVERT: C  287 TYR cc_start: 0.8905 (t80) cc_final: 0.8240 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0976
  time to fit residues: 32.7473
Evaluate side-chains
  178 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 135 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   chunk 134 optimal weight:    0.8980
   chunk 114 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.108936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.086738 restraints weight = 23245.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.089800 restraints weight = 13450.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.091843 restraints weight = 9363.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.093065 restraints weight = 7354.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.094017 restraints weight = 6300.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12855  Z= 0.107
  Angle     :  0.473   5.405  17490  Z= 0.254
  Chirality :  0.047   0.144   2016
  Planarity :  0.004   0.038   2235
  Dihedral  :  4.176  16.410   1725
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.87 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  0.10 (0.22), residues: 1569
  helix:  0.20 (0.36), residues: 237
  sheet:  0.50 (0.24), residues: 456
  loop : -0.12 (0.22), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 446 
 TYR   0.016   0.001   TYR A 287 
 PHE   0.016   0.001   PHE A 199 
 TRP   0.007   0.001   TRP C 108 
 HIS   0.003   0.001   HIS C 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12855)
  covalent geometry    : angle       0.47261 (17490)
  hydrogen bonds       : bond        0.03201 (  455)
  hydrogen bonds       : angle       4.91893 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8347 (m-30) cc_final: 0.7978 (m-30)
REVERT: A  218 MET cc_start: 0.7806 (mpp) cc_final: 0.7516 (mpp)
REVERT: A  282 ASP cc_start: 0.8679 (m-30) cc_final: 0.8444 (m-30)
REVERT: A  432 ASP cc_start: 0.8467 (p0) cc_final: 0.7851 (p0)
REVERT: A  434 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8875 (mmtp)
REVERT: B  284 ILE cc_start: 0.9104 (mt) cc_final: 0.8852 (mm)
REVERT: B  424 ASN cc_start: 0.8240 (m-40) cc_final: 0.7947 (t0)
REVERT: B  436 LYS cc_start: 0.8792 (tptp) cc_final: 0.8465 (tppp)
REVERT: B  539 GLN cc_start: 0.8230 (mp10) cc_final: 0.7739 (mp10)
REVERT: C  218 MET cc_start: 0.7920 (mpp) cc_final: 0.7530 (mpp)
REVERT: C  282 ASP cc_start: 0.8636 (m-30) cc_final: 0.8430 (m-30)
REVERT: C  287 TYR cc_start: 0.8849 (t80) cc_final: 0.8300 (t80)
REVERT: C  432 ASP cc_start: 0.8543 (p0) cc_final: 0.8321 (p0)
REVERT: C  500 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6402 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0922
  time to fit residues: 31.8076
Evaluate side-chains
  180 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 125 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 123 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 142 optimal weight:    0.0030
   chunk 98 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.6390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.109960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.087855 restraints weight = 23250.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.090939 restraints weight = 13219.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.092897 restraints weight = 9134.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.094374 restraints weight = 7183.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.095131 restraints weight = 6055.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12855  Z= 0.095
  Angle     :  0.463   5.463  17490  Z= 0.247
  Chirality :  0.046   0.145   2016
  Planarity :  0.004   0.034   2235
  Dihedral  :  4.029  16.517   1725
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.49 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.22 (0.22), residues: 1569
  helix:  0.23 (0.37), residues: 237
  sheet:  0.58 (0.24), residues: 456
  loop : -0.02 (0.22), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 446 
 TYR   0.015   0.001   TYR A 287 
 PHE   0.016   0.001   PHE C 199 
 TRP   0.007   0.001   TRP C 108 
 HIS   0.002   0.000   HIS C 386 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (12855)
  covalent geometry    : angle       0.46336 (17490)
  hydrogen bonds       : bond        0.03020 (  455)
  hydrogen bonds       : angle       4.81068 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8306 (m-30) cc_final: 0.7945 (m-30)
REVERT: A  218 MET cc_start: 0.7853 (mpp) cc_final: 0.7569 (mpp)
REVERT: A  282 ASP cc_start: 0.8672 (m-30) cc_final: 0.8449 (m-30)
REVERT: A  287 TYR cc_start: 0.8731 (t80) cc_final: 0.8404 (t80)
REVERT: A  392 ASP cc_start: 0.7791 (t0) cc_final: 0.7517 (t0)
REVERT: A  432 ASP cc_start: 0.8468 (p0) cc_final: 0.7765 (p0)
REVERT: A  434 LYS cc_start: 0.9162 (mmmt) cc_final: 0.8860 (mmtp)
REVERT: A  539 GLN cc_start: 0.8173 (mp10) cc_final: 0.7937 (mp10)
REVERT: B  284 ILE cc_start: 0.9075 (mt) cc_final: 0.8821 (mm)
REVERT: B  424 ASN cc_start: 0.8209 (m-40) cc_final: 0.8005 (t0)
REVERT: B  436 LYS cc_start: 0.8799 (tptp) cc_final: 0.8414 (tppp)
REVERT: B  482 THR cc_start: 0.7719 (p) cc_final: 0.7511 (p)
REVERT: B  539 GLN cc_start: 0.8217 (mp10) cc_final: 0.7827 (mp10)
REVERT: C  218 MET cc_start: 0.7825 (mpp) cc_final: 0.7459 (mpp)
REVERT: C  287 TYR cc_start: 0.8855 (t80) cc_final: 0.8392 (t80)
REVERT: C  383 HIS cc_start: 0.8197 (t-90) cc_final: 0.7878 (t70)
REVERT: C  500 LYS cc_start: 0.6733 (ptpt) cc_final: 0.6212 (pttp)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0889
  time to fit residues: 31.5149
Evaluate side-chains
  183 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 126 optimal weight:    5.9990
   chunk 138 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 152 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.108869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.086504 restraints weight = 23604.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.089559 restraints weight = 13559.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.091623 restraints weight = 9421.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.092791 restraints weight = 7381.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.093794 restraints weight = 6350.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12855  Z= 0.134
  Angle     :  0.490   6.147  17490  Z= 0.262
  Chirality :  0.047   0.142   2016
  Planarity :  0.004   0.059   2235
  Dihedral  :  4.088  16.832   1725
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.80 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.25 (0.22), residues: 1569
  helix:  0.29 (0.37), residues: 237
  sheet:  0.61 (0.24), residues: 462
  loop : -0.02 (0.22), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 446 
 TYR   0.018   0.001   TYR A 287 
 PHE   0.017   0.001   PHE B 199 
 TRP   0.004   0.001   TRP B 108 
 HIS   0.002   0.000   HIS C 344 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12855)
  covalent geometry    : angle       0.49004 (17490)
  hydrogen bonds       : bond        0.03365 (  455)
  hydrogen bonds       : angle       4.87407 ( 1365)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ASP cc_start: 0.8342 (m-30) cc_final: 0.7980 (m-30)
REVERT: A  165 GLU cc_start: 0.7665 (tp30) cc_final: 0.7375 (tp30)
REVERT: A  218 MET cc_start: 0.7829 (mpp) cc_final: 0.7548 (mpp)
REVERT: A  282 ASP cc_start: 0.8759 (m-30) cc_final: 0.8531 (m-30)
REVERT: A  424 ASN cc_start: 0.8638 (t0) cc_final: 0.8099 (t0)
REVERT: A  432 ASP cc_start: 0.8387 (p0) cc_final: 0.7752 (p0)
REVERT: A  434 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8859 (mmtp)
REVERT: A  482 THR cc_start: 0.7733 (p) cc_final: 0.7532 (p)
REVERT: B  284 ILE cc_start: 0.9100 (mt) cc_final: 0.8849 (mm)
REVERT: B  424 ASN cc_start: 0.8226 (m-40) cc_final: 0.7945 (t0)
REVERT: B  436 LYS cc_start: 0.8815 (tptp) cc_final: 0.8467 (tppp)
REVERT: B  500 LYS cc_start: 0.7284 (ptpt) cc_final: 0.6884 (pttm)
REVERT: C  218 MET cc_start: 0.7896 (mpp) cc_final: 0.7550 (mpp)
REVERT: C  282 ASP cc_start: 0.8655 (m-30) cc_final: 0.8446 (m-30)
REVERT: C  287 TYR cc_start: 0.8901 (t80) cc_final: 0.8298 (t80)
REVERT: C  500 LYS cc_start: 0.6789 (ptpt) cc_final: 0.6421 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0947
  time to fit residues: 31.4995
Evaluate side-chains
  173 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 105 optimal weight:    0.1980
   chunk 61 optimal weight:    1.9990
   chunk 145 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 124 optimal weight:    0.0470
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
C 383 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.110744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.088621 restraints weight = 23343.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.091687 restraints weight = 13306.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.093762 restraints weight = 9204.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.095167 restraints weight = 7189.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.096086 restraints weight = 6079.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12855  Z= 0.090
  Angle     :  0.466   5.451  17490  Z= 0.248
  Chirality :  0.046   0.145   2016
  Planarity :  0.004   0.034   2235
  Dihedral  :  3.935  16.901   1725
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.61 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  0.31 (0.22), residues: 1569
  helix:  0.27 (0.36), residues: 237
  sheet:  0.65 (0.24), residues: 456
  loop :  0.05 (0.22), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 446 
 TYR   0.015   0.001   TYR A 287 
 PHE   0.016   0.001   PHE B 199 
 TRP   0.007   0.001   TRP C 108 
 HIS   0.002   0.001   HIS C 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 (12855)
  covalent geometry    : angle       0.46566 (17490)
  hydrogen bonds       : bond        0.02976 (  455)
  hydrogen bonds       : angle       4.77940 ( 1365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1799.79 seconds
wall clock time: 32 minutes 7.86 seconds (1927.86 seconds total)