Starting phenix.real_space_refine
on Wed Mar  4 09:51:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfe_31950/03_2026/7vfe_31950.cif"
  }
  resolution = 2.63
  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    8079      2.51       5
     N    2052      2.21       5
     O    2463      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 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: 12630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4210
          Classifications: {'peptide': 529}
          Link IDs: {'PTRANS': 25, 'TRANS': 503}
          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: 3.00, per 1000 atoms: 0.24
  Number of scatterers: 12630
  At special positions: 0
  Unit cell: (99.456, 102.564, 111.888, 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    2463      8.00
     N    2052      7.00
     C    8079      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: 0.95
  Conformation dependent library (CDL) restraints added in 597.0 milliseconds
  

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3024

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 36 sheets defined
      19.8% alpha, 42.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  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: 3.800A  pdb=" N   VAL A 164 " --> pdb=" O   PRO A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 169
    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: 4.127A  pdb=" N   ASP A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ASP A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 394
      removed outlier: 3.590A  pdb=" N   THR A 393 " --> pdb=" O   ASN A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
      removed outlier: 3.777A  pdb=" N   TRP A 400 " --> pdb=" O   PRO A 396 " (cutoff:3.500A)
      removed outlier: 3.912A  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: 3.801A  pdb=" N   VAL B 164 " --> pdb=" O   PRO B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 169
    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: 4.127A  pdb=" N   ASP B 293 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ASP B 294 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 394
      removed outlier: 3.591A  pdb=" N   THR B 393 " --> pdb=" O   ASN B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
      removed outlier: 3.778A  pdb=" N   TRP B 400 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
      removed outlier: 3.912A  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: 3.801A  pdb=" N   VAL C 164 " --> pdb=" O   PRO C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 169
    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: 4.127A  pdb=" N   ASP C 293 " --> pdb=" O   SER C 289 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ASP C 294 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 389 through 394
      removed outlier: 3.592A  pdb=" N   THR C 393 " --> pdb=" O   ASN C 389 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 396 through 401
      removed outlier: 3.777A  pdb=" N   TRP C 400 " --> pdb=" O   PRO C 396 " (cutoff:3.500A)
      removed outlier: 3.912A  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: 3.918A  pdb=" N   ILE A 215 " --> pdb=" O   HIS A  68 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   HIS A  68 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU A  66 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
      removed outlier: 4.157A  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: 3.918A  pdb=" N   ILE A 215 " --> pdb=" O   HIS A  68 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   HIS A  68 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   TYR A 217 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 5.905A  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: 6.656A  pdb=" N   THR A 179 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ILE A 100 " --> pdb=" O   THR A 179 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   THR A 181 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   VAL A  98 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR A 183 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ASN A  96 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   GLU A 111 " --> pdb=" O   ASN A  96 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL A  98 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   GLU A 109 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE A 100 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY A 105 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79
      removed outlier: 6.607A  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
    Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236
      removed outlier: 3.968A  pdb=" N   GLN A 522 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER A 254 " --> pdb=" O   ASN A 530 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU A 532 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA A 252 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 3.519A  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: 3.663A  pdb=" N   ARG A 475 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA A 252 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU A 532 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER A 254 " --> pdb=" O   ASN A 530 " (cutoff:3.500A)
      removed outlier: 3.968A  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: 6.426A  pdb=" N   LYS A 502 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   SER A 504 " --> pdb=" O   VAL A 445 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL A 445 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG A 506 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   LEU A 443 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL A 508 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   PHE A 447 " --> pdb=" O   VAL A 451 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   VAL A 451 " --> pdb=" O   PHE A 447 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 270
    Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 299
    Processing sheet with id=AB2, first strand: chain 'A' and resid 320 through 322
      removed outlier: 6.779A  pdb=" N   ASP A 327 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   ILE A 368 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   TYR A 329 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   GLY A 370 " --> pdb=" O   TYR A 329 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LYS A 331 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
      removed outlier: 7.634A  pdb=" N   TYR A 372 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASP A 333 " --> pdb=" O   TYR A 372 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   PHE A 365 " --> pdb=" O   HIS A 386 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   HIS A 386 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA A 367 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ILE A 384 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR A 369 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 350
    Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40
      removed outlier: 3.917A  pdb=" N   ILE B 215 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   HIS B  68 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU B  66 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU B  69 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 40
      removed outlier: 3.917A  pdb=" N   ILE B 215 " --> pdb=" O   HIS B  68 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   HIS B  68 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   TYR B 217 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU B  66 " --> pdb=" O   TYR B 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 44
      removed outlier: 6.656A  pdb=" N   THR B 179 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ILE B 100 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   THR B 181 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   VAL B  98 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR B 183 " --> pdb=" O   ASN B  96 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ASN B  96 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   GLU B 111 " --> pdb=" O   ASN B  96 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL B  98 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   GLU B 109 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE B 100 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY B 105 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 78 through 79
      removed outlier: 6.608A  pdb=" N   VAL B  78 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 139 through 141
    Processing sheet with id=AB9, first strand: chain 'B' and resid 227 through 236
      removed outlier: 3.968A  pdb=" N   GLN B 522 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER B 254 " --> pdb=" O   ASN B 530 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU B 532 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA B 252 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478
      removed outlier: 3.663A  pdb=" N   ARG B 475 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LEU B 532 " --> pdb=" O   ALA B 252 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER B 254 " --> pdb=" O   ASN B 530 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN B 522 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 243 through 247
      removed outlier: 6.426A  pdb=" N   LYS B 502 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   PHE B 447 " --> pdb=" O   LYS B 502 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER B 504 " --> pdb=" O   VAL B 445 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL B 445 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG B 506 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   LEU B 443 " --> pdb=" O   ARG B 506 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL B 508 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   PHE B 447 " --> pdb=" O   VAL B 451 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   VAL B 451 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270
    Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 299
    Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 322
      removed outlier: 6.779A  pdb=" N   ASP B 327 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ILE B 368 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   TYR B 329 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLY B 370 " --> pdb=" O   TYR B 329 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LYS B 331 " --> pdb=" O   GLY B 370 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   TYR B 372 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASP B 333 " --> pdb=" O   TYR B 372 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   PHE B 365 " --> pdb=" O   HIS B 386 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   HIS B 386 " --> pdb=" O   PHE B 365 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ALA B 367 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ILE B 384 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR B 369 " --> pdb=" O   ALA B 382 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 349 through 350
    Processing sheet with id=AC7, first strand: chain 'C' and resid 32 through 40
      removed outlier: 3.916A  pdb=" N   ILE C 215 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU C  66 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU C  69 " --> pdb=" O   ILE C 158 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 40
      removed outlier: 3.916A  pdb=" N   ILE C 215 " --> pdb=" O   HIS C  68 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   HIS C  68 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   TYR C 217 " --> pdb=" O   LEU C  66 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LEU C  66 " --> pdb=" O   TYR C 217 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 42 through 44
      removed outlier: 6.657A  pdb=" N   THR C 179 " --> pdb=" O   ILE C 100 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ILE C 100 " --> pdb=" O   THR C 179 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   THR C 181 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL C  98 " --> pdb=" O   THR C 181 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR C 183 " --> pdb=" O   ASN C  96 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ASN C  96 " --> pdb=" O   GLU C 111 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   GLU C 111 " --> pdb=" O   ASN C  96 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL C  98 " --> pdb=" O   GLU C 109 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLU C 109 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE C 100 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY C 105 " --> pdb=" O   SER C 102 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 78 through 79
      removed outlier: 6.607A  pdb=" N   VAL C  78 " --> pdb=" O   ILE C 148 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 139 through 141
    Processing sheet with id=AD3, first strand: chain 'C' and resid 227 through 236
      removed outlier: 3.968A  pdb=" N   GLN C 522 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER C 254 " --> pdb=" O   ASN C 530 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU C 532 " --> pdb=" O   ALA C 252 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA C 252 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA C 252 " --> pdb=" O   ILE C 492 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 475 through 478
      removed outlier: 3.662A  pdb=" N   ARG C 475 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA C 252 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU C 532 " --> pdb=" O   ALA C 252 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   SER C 254 " --> pdb=" O   ASN C 530 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN C 522 " --> pdb=" O   TYR C 262 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 243 through 247
      removed outlier: 6.427A  pdb=" N   LYS C 502 " --> pdb=" O   PHE C 447 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   PHE C 447 " --> pdb=" O   LYS C 502 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER C 504 " --> pdb=" O   VAL C 445 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL C 445 " --> pdb=" O   SER C 504 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ARG C 506 " --> pdb=" O   LEU C 443 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LEU C 443 " --> pdb=" O   ARG C 506 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL C 508 " --> pdb=" O   SER C 441 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   PHE C 447 " --> pdb=" O   VAL C 451 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   VAL C 451 " --> pdb=" O   PHE C 447 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 269 through 270
    Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 299
    Processing sheet with id=AD8, first strand: chain 'C' and resid 320 through 322
      removed outlier: 6.779A  pdb=" N   ASP C 327 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   ILE C 368 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   TYR C 329 " --> pdb=" O   ILE C 368 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   GLY C 370 " --> pdb=" O   TYR C 329 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LYS C 331 " --> pdb=" O   GLY C 370 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   TYR C 372 " --> pdb=" O   LYS C 331 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ASP C 333 " --> pdb=" O   TYR C 372 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   PHE C 365 " --> pdb=" O   HIS C 386 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   HIS C 386 " --> pdb=" O   PHE C 365 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ALA C 367 " --> pdb=" O   ILE C 384 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ILE C 384 " --> pdb=" O   ALA C 367 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   THR C 369 " --> pdb=" O   ALA C 382 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 349 through 350

    480 hydrogen bonds defined for protein.
    1251 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: 2.21

  Time building geometry restraints manager: 1.34 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: 4026
        1.34 -     1.45: 2308
        1.45 -     1.57: 6512
        1.57 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 12906
  Sorted by residual:
  bond pdb=" CB  CYS C  94 "
       pdb=" SG  CYS C  94 "
    ideal  model  delta    sigma   weight residual
    1.808  1.749  0.059 3.30e-02 9.18e+02 3.21e+00
  bond pdb=" CB  CYS B  94 "
       pdb=" SG  CYS B  94 "
    ideal  model  delta    sigma   weight residual
    1.808  1.749  0.059 3.30e-02 9.18e+02 3.20e+00
  bond pdb=" CB  CYS A  94 "
       pdb=" SG  CYS A  94 "
    ideal  model  delta    sigma   weight residual
    1.808  1.750  0.058 3.30e-02 9.18e+02 3.09e+00
  bond pdb=" CA  ASN C  45 "
       pdb=" CB  ASN C  45 "
    ideal  model  delta    sigma   weight residual
    1.530  1.497  0.033 2.00e-02 2.50e+03 2.72e+00
  bond pdb=" CA  ASN A  45 "
       pdb=" CB  ASN A  45 "
    ideal  model  delta    sigma   weight residual
    1.530  1.497  0.033 2.00e-02 2.50e+03 2.68e+00
  ... (remaining 12901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 16983
        1.35 -     2.71: 473
        2.71 -     4.06: 87
        4.06 -     5.41: 4
        5.41 -     6.77: 9
  Bond angle restraints: 17556
  Sorted by residual:
  angle pdb=" N   ILE A 395 "
        pdb=" CA  ILE A 395 "
        pdb=" C   ILE A 395 "
      ideal   model   delta    sigma   weight residual
     108.95  113.29   -4.34 9.80e-01 1.04e+00 1.96e+01
  angle pdb=" N   ILE C 395 "
        pdb=" CA  ILE C 395 "
        pdb=" C   ILE C 395 "
      ideal   model   delta    sigma   weight residual
     108.95  113.29   -4.34 9.80e-01 1.04e+00 1.96e+01
  angle pdb=" N   ILE B 395 "
        pdb=" CA  ILE B 395 "
        pdb=" C   ILE B 395 "
      ideal   model   delta    sigma   weight residual
     108.95  113.27   -4.32 9.80e-01 1.04e+00 1.94e+01
  angle pdb=" CA  LYS A  93 "
        pdb=" CB  LYS A  93 "
        pdb=" CG  LYS A  93 "
      ideal   model   delta    sigma   weight residual
     114.10  110.11    3.99 2.00e+00 2.50e-01 3.98e+00
  angle pdb=" CA  LYS C  93 "
        pdb=" CB  LYS C  93 "
        pdb=" CG  LYS C  93 "
      ideal   model   delta    sigma   weight residual
     114.10  110.12    3.98 2.00e+00 2.50e-01 3.96e+00
  ... (remaining 17551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 7144
       17.99 -    35.98: 455
       35.98 -    53.98: 123
       53.98 -    71.97: 22
       71.97 -    89.96: 11
  Dihedral angle restraints: 7755
    sinusoidal: 3054
      harmonic: 4701
  Sorted by residual:
  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 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  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 -160.79  -19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  TYR B 407 "
           pdb=" C   TYR B 407 "
           pdb=" N   ASN B 408 "
           pdb=" CA  ASN B 408 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.80   19.20     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 7752 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 817
       0.028 -    0.056: 598
       0.056 -    0.084: 350
       0.084 -    0.112: 209
       0.112 -    0.140: 51
  Chirality restraints: 2025
  Sorted by residual:
  chirality pdb=" CA  LYS B  93 "
            pdb=" N   LYS B  93 "
            pdb=" C   LYS B  93 "
            pdb=" CB  LYS B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  LYS C  93 "
            pdb=" N   LYS C  93 "
            pdb=" C   LYS C  93 "
            pdb=" CB  LYS C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  LYS A  93 "
            pdb=" N   LYS A  93 "
            pdb=" C   LYS A  93 "
            pdb=" CB  LYS A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 2022 not shown)

  Planarity restraints: 2241
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 209 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.01e+00
        pdb=" N   PRO A 210 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 209 "   -0.037 5.00e-02 4.00e+02   5.56e-02 4.94e+00
        pdb=" N   PRO B 210 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO B 210 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 210 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 209 "    0.037 5.00e-02 4.00e+02   5.55e-02 4.94e+00
        pdb=" N   PRO C 210 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO C 210 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 210 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2238 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3531
        2.81 -     3.33: 10626
        3.33 -     3.85: 22044
        3.85 -     4.38: 25568
        4.38 -     4.90: 43320
  Nonbonded interactions: 105089
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 322 "
            pdb=" OD1 ASP A 327 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER B 322 "
            pdb=" OD1 ASP B 327 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER C 322 "
            pdb=" OD1 ASP C 327 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG1 THR C 352 "
            pdb=" OD1 ASN C 515 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" OG1 THR B 352 "
            pdb=" OD1 ASN B 515 "
     model   vdw
     2.392 3.040
  ... (remaining 105084 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.340
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
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      :  0.008   0.059  12906  Z= 0.325
  Angle     :  0.582   6.768  17556  Z= 0.322
  Chirality :  0.053   0.140   2025
  Planarity :  0.005   0.056   2241
  Dihedral  : 13.518  89.962   4731
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  :  8.83 %
    Favored  : 88.09 %
  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: -0.79 (0.19), residues: 1575
  helix: -1.39 (0.29), residues: 228
  sheet:  0.34 (0.23), residues: 468
  loop : -0.71 (0.19), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 475 
 TYR   0.014   0.002   TYR A 463 
 PHE   0.016   0.002   PHE A  84 
 TRP   0.006   0.002   TRP A 108 
 HIS   0.004   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00782 (12906)
  covalent geometry    : angle       0.58197 (17556)
  hydrogen bonds       : bond        0.14804 (  420)
  hydrogen bonds       : angle       7.23176 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 184
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  547 MET cc_start: 0.7797 (mmt) cc_final: 0.7338 (mmt)
REVERT: C   33 MET cc_start: 0.8670 (tpt) cc_final: 0.8375 (tpp)
REVERT: C   62 TYR cc_start: 0.7645 (m-80) cc_final: 0.7321 (m-80)
REVERT: C  471 ASN cc_start: 0.8197 (m-40) cc_final: 0.7894 (m-40)
  outliers start: 45
  outliers final: 22
  residues processed: 223
  average time/residue: 0.6018
  time to fit residues: 145.4895
Evaluate side-chains
  139 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 SER
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   26 SER
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  266 THR
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
B  61 GLN
B 403 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.092244 restraints weight = 15295.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.80
r_work: 0.2868 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  12906  Z= 0.110
  Angle     :  0.478   7.762  17556  Z= 0.256
  Chirality :  0.047   0.170   2025
  Planarity :  0.004   0.045   2241
  Dihedral  :  5.743  85.627   1754
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.42 %
    Favored  : 84.05 %
  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 (0.20), residues: 1575
  helix: -0.32 (0.34), residues: 231
  sheet:  0.66 (0.23), residues: 468
  loop : -0.33 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 234 
 TYR   0.011   0.001   TYR C 520 
 PHE   0.012   0.001   PHE C 199 
 TRP   0.004   0.001   TRP A 108 
 HIS   0.003   0.001   HIS C 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (12906)
  covalent geometry    : angle       0.47798 (17556)
  hydrogen bonds       : bond        0.03714 (  420)
  hydrogen bonds       : angle       5.12545 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8866 (mtm) cc_final: 0.8666 (mtp)
REVERT: A  547 MET cc_start: 0.8145 (mmt) cc_final: 0.7783 (mmt)
REVERT: B  205 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7779 (mm-30)
REVERT: B  324 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6039 (mp10)
REVERT: C   74 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8470 (mt-10)
REVERT: C  220 LYS cc_start: 0.8190 (mppt) cc_final: 0.7748 (mmtp)
REVERT: C  471 ASN cc_start: 0.8701 (m-40) cc_final: 0.8322 (m-40)
REVERT: C  524 GLN cc_start: 0.9149 (mt0) cc_final: 0.8836 (mt0)
  outliers start: 37
  outliers final: 18
  residues processed: 172
  average time/residue: 0.5605
  time to fit residues: 105.1262
Evaluate side-chains
  145 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain B residue   17 LYS
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  454 SER
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  148 ILE
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  454 SER
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 112 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 138 optimal weight:    6.9990
   chunk 59 optimal weight:    0.1980
   chunk 103 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 120 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 130 optimal weight:    4.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  61 GLN
C 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.092689 restraints weight = 15682.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.81
r_work: 0.2892 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12906  Z= 0.093
  Angle     :  0.450   9.134  17556  Z= 0.236
  Chirality :  0.046   0.159   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.760  57.500   1743
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.26 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.21), residues: 1575
  helix:  0.15 (0.36), residues: 231
  sheet:  0.78 (0.24), residues: 468
  loop : -0.06 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 234 
 TYR   0.009   0.001   TYR B 520 
 PHE   0.010   0.001   PHE C 199 
 TRP   0.004   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (12906)
  covalent geometry    : angle       0.45009 (17556)
  hydrogen bonds       : bond        0.03210 (  420)
  hydrogen bonds       : angle       4.67929 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7891 (tp30)
REVERT: A  547 MET cc_start: 0.8197 (mmt) cc_final: 0.7870 (mmt)
REVERT: B   25 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7329 (p0)
REVERT: B   27 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8711 (mt0)
REVERT: B  205 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7930 (mm-30)
REVERT: B  220 LYS cc_start: 0.8205 (mptt) cc_final: 0.7953 (mptt)
REVERT: B  325 ASP cc_start: 0.7213 (p0) cc_final: 0.6851 (p0)
REVERT: C   27 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8748 (mt0)
REVERT: C  127 LYS cc_start: 0.8904 (tptt) cc_final: 0.8597 (tptt)
REVERT: C  220 LYS cc_start: 0.8277 (mppt) cc_final: 0.7875 (mmtp)
REVERT: C  378 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7622 (mtm180)
REVERT: C  471 ASN cc_start: 0.8627 (m-40) cc_final: 0.8315 (m-40)
  outliers start: 30
  outliers final: 18
  residues processed: 154
  average time/residue: 0.5882
  time to fit residues: 98.5030
Evaluate side-chains
  146 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  482 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 152 optimal weight:    2.9990
   chunk 154 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.106929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.088436 restraints weight = 15602.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.81
r_work: 0.2803 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12906  Z= 0.246
  Angle     :  0.554   8.499  17556  Z= 0.290
  Chirality :  0.051   0.147   2025
  Planarity :  0.004   0.053   2241
  Dihedral  :  4.913  54.383   1738
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.44 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.21), residues: 1575
  helix:  0.12 (0.35), residues: 228
  sheet:  0.84 (0.25), residues: 432
  loop :  0.01 (0.20), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 290 
 TYR   0.015   0.002   TYR C 520 
 PHE   0.015   0.002   PHE B 199 
 TRP   0.007   0.002   TRP A 108 
 HIS   0.006   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (12906)
  covalent geometry    : angle       0.55405 (17556)
  hydrogen bonds       : bond        0.04479 (  420)
  hydrogen bonds       : angle       5.06338 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 121
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8501 (mt-10)
REVERT: A  113 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7901 (tp30)
REVERT: B   25 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7292 (m-30)
REVERT: B   27 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8779 (mt0)
REVERT: B  113 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8623 (tp30)
REVERT: B  205 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8029 (mm-30)
REVERT: B  220 LYS cc_start: 0.8234 (mptt) cc_final: 0.7997 (mptt)
REVERT: C   27 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8762 (mt0)
REVERT: C   74 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8431 (mt-10)
REVERT: C  220 LYS cc_start: 0.8318 (mppt) cc_final: 0.7884 (mmtp)
  outliers start: 42
  outliers final: 23
  residues processed: 152
  average time/residue: 0.5890
  time to fit residues: 97.2860
Evaluate side-chains
  149 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 132 optimal weight:    0.0470
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 150 optimal weight:    0.0970
   chunk 115 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 139 optimal weight:    6.9990
   overall best weight:    1.0080

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

Flipped N/Q/H residues before XYZ refinement:
C 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.108828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.090516 restraints weight = 15694.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.81
r_work: 0.2869 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12906  Z= 0.125
  Angle     :  0.475   9.341  17556  Z= 0.248
  Chirality :  0.047   0.130   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.632  55.925   1738
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.06 %
    Favored  : 82.55 %
  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:  0.34 (0.21), residues: 1575
  helix:  0.20 (0.36), residues: 231
  sheet:  0.76 (0.24), residues: 468
  loop :  0.04 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 234 
 TYR   0.011   0.001   TYR B 520 
 PHE   0.013   0.001   PHE C 199 
 TRP   0.004   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12906)
  covalent geometry    : angle       0.47550 (17556)
  hydrogen bonds       : bond        0.03430 (  420)
  hydrogen bonds       : angle       4.76854 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (mt-10)
REVERT: A  113 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7868 (tp30)
REVERT: A  218 MET cc_start: 0.8713 (mmt) cc_final: 0.8316 (mmt)
REVERT: B   25 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7343 (m-30)
REVERT: B   27 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8732 (mt0)
REVERT: B  113 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8451 (tt0)
REVERT: B  175 ASP cc_start: 0.8564 (m-30) cc_final: 0.8259 (m-30)
REVERT: B  205 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8024 (mm-30)
REVERT: B  220 LYS cc_start: 0.8213 (mptt) cc_final: 0.7963 (mptt)
REVERT: B  325 ASP cc_start: 0.7626 (p0) cc_final: 0.7315 (p0)
REVERT: C   27 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8802 (mt0)
REVERT: C  220 LYS cc_start: 0.8294 (mppt) cc_final: 0.7892 (mmtp)
REVERT: C  380 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8421 (pp)
  outliers start: 35
  outliers final: 21
  residues processed: 153
  average time/residue: 0.5986
  time to fit residues: 99.5117
Evaluate side-chains
  147 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  380 ILE
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 146 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 155 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0670
   overall best weight:    1.9524

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.106575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.087902 restraints weight = 15738.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.89
r_work: 0.2795 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2668 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12906  Z= 0.206
  Angle     :  0.529   8.885  17556  Z= 0.277
  Chirality :  0.049   0.149   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.844  56.055   1738
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.85 %
    Favored  : 82.14 %
  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:  0.32 (0.21), residues: 1575
  helix:  0.21 (0.36), residues: 228
  sheet:  0.70 (0.24), residues: 462
  loop :  0.04 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.014   0.002   TYR B 520 
 PHE   0.014   0.002   PHE C 199 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00494 (12906)
  covalent geometry    : angle       0.52930 (17556)
  hydrogen bonds       : bond        0.04104 (  420)
  hydrogen bonds       : angle       4.93884 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 116
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8528 (mt-10)
REVERT: A  113 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.7868 (tp30)
REVERT: A  431 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8655 (pp)
REVERT: B   25 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (m-30)
REVERT: B   27 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8760 (mt0)
REVERT: B  113 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8581 (tt0)
REVERT: B  175 ASP cc_start: 0.8616 (m-30) cc_final: 0.8321 (m-30)
REVERT: B  205 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8037 (mm-30)
REVERT: B  220 LYS cc_start: 0.8215 (mptt) cc_final: 0.7968 (mptt)
REVERT: B  325 ASP cc_start: 0.7719 (p0) cc_final: 0.7413 (p0)
REVERT: C   27 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8818 (mt0)
REVERT: C  127 LYS cc_start: 0.8954 (tptt) cc_final: 0.8654 (tptt)
REVERT: C  220 LYS cc_start: 0.8291 (mppt) cc_final: 0.7842 (mmtp)
  outliers start: 44
  outliers final: 23
  residues processed: 150
  average time/residue: 0.5992
  time to fit residues: 97.4522
Evaluate side-chains
  145 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 145 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 142 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN
C 334 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.107443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.089262 restraints weight = 15711.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.80
r_work: 0.2836 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12906  Z= 0.187
  Angle     :  0.522  10.168  17556  Z= 0.272
  Chirality :  0.049   0.156   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.802  56.175   1738
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.40 %
    Favored  : 81.93 %
  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:  0.34 (0.21), residues: 1575
  helix:  0.22 (0.36), residues: 228
  sheet:  0.68 (0.24), residues: 462
  loop :  0.08 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 290 
 TYR   0.014   0.002   TYR B 520 
 PHE   0.013   0.002   PHE C 199 
 TRP   0.005   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (12906)
  covalent geometry    : angle       0.52231 (17556)
  hydrogen bonds       : bond        0.03897 (  420)
  hydrogen bonds       : angle       4.89733 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7980 (tm-30)
REVERT: A   74 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (mt-10)
REVERT: A  113 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.7876 (tp30)
REVERT: A  431 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8734 (pp)
REVERT: B   25 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (m-30)
REVERT: B   27 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8772 (mt0)
REVERT: B  113 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8546 (tt0)
REVERT: B  175 ASP cc_start: 0.8580 (m-30) cc_final: 0.8301 (m-30)
REVERT: B  205 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8047 (mm-30)
REVERT: B  220 LYS cc_start: 0.8239 (mptt) cc_final: 0.7991 (mptt)
REVERT: B  325 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7641 (p0)
REVERT: C   27 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8867 (mt0)
REVERT: C   74 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8444 (mt-10)
REVERT: C  220 LYS cc_start: 0.8348 (mppt) cc_final: 0.7894 (mmtp)
  outliers start: 39
  outliers final: 20
  residues processed: 146
  average time/residue: 0.6228
  time to fit residues: 98.5577
Evaluate side-chains
  145 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 GLN
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0870
   chunk 138 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.6166

-------------------------------------------------------------------------------
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 = 0.3229 r_free = 0.3229 target = 0.107498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.089424 restraints weight = 15529.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.78
r_work: 0.2847 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12906  Z= 0.177
  Angle     :  0.515  10.363  17556  Z= 0.269
  Chirality :  0.048   0.153   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.749  56.245   1735
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.26 %
    Favored  : 82.07 %
  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:  0.35 (0.21), residues: 1575
  helix:  0.23 (0.36), residues: 228
  sheet:  0.68 (0.24), residues: 462
  loop :  0.09 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 290 
 TYR   0.013   0.001   TYR B 520 
 PHE   0.013   0.001   PHE C 199 
 TRP   0.006   0.001   TRP A 108 
 HIS   0.003   0.001   HIS C 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (12906)
  covalent geometry    : angle       0.51488 (17556)
  hydrogen bonds       : bond        0.03824 (  420)
  hydrogen bonds       : angle       4.88113 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.556 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8495 (mt-10)
REVERT: A  113 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.7867 (tp30)
REVERT: A  166 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7844 (m-30)
REVERT: A  431 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8726 (pp)
REVERT: B   25 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7512 (m-30)
REVERT: B   27 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8794 (mt0)
REVERT: B  113 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8539 (tt0)
REVERT: B  175 ASP cc_start: 0.8564 (m-30) cc_final: 0.8287 (m-30)
REVERT: B  205 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (mm-30)
REVERT: B  220 LYS cc_start: 0.8213 (mptt) cc_final: 0.7948 (mptt)
REVERT: C   27 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8821 (mt0)
REVERT: C  127 LYS cc_start: 0.8954 (tptt) cc_final: 0.8744 (tptt)
REVERT: C  220 LYS cc_start: 0.8345 (mppt) cc_final: 0.7894 (mmtp)
  outliers start: 39
  outliers final: 23
  residues processed: 148
  average time/residue: 0.6155
  time to fit residues: 98.6671
Evaluate side-chains
  146 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  200 GLU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 120 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3242 r_free = 0.3242 target = 0.108469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.090391 restraints weight = 15618.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.80
r_work: 0.2841 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8763
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12906  Z= 0.133
  Angle     :  0.501  10.735  17556  Z= 0.261
  Chirality :  0.047   0.134   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.606  57.373   1735
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.67 %
    Favored  : 82.00 %
  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:  0.41 (0.21), residues: 1575
  helix:  0.25 (0.36), residues: 231
  sheet:  0.69 (0.24), residues: 462
  loop :  0.17 (0.21), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 404 
 TYR   0.014   0.001   TYR C 520 
 PHE   0.013   0.001   PHE C 357 
 TRP   0.005   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (12906)
  covalent geometry    : angle       0.50131 (17556)
  hydrogen bonds       : bond        0.03431 (  420)
  hydrogen bonds       : angle       4.76615 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8487 (mt-10)
REVERT: A  113 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7860 (tp30)
REVERT: A  431 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8714 (pp)
REVERT: B   25 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7508 (m-30)
REVERT: B   27 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8859 (mt0)
REVERT: B  113 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8478 (tt0)
REVERT: B  175 ASP cc_start: 0.8559 (m-30) cc_final: 0.8284 (m-30)
REVERT: B  205 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8058 (mm-30)
REVERT: B  220 LYS cc_start: 0.8216 (mptt) cc_final: 0.7948 (mptt)
REVERT: C   27 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8859 (mt0)
REVERT: C   74 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8449 (mt-10)
REVERT: C  220 LYS cc_start: 0.8343 (mppt) cc_final: 0.7901 (mmtp)
  outliers start: 34
  outliers final: 24
  residues processed: 147
  average time/residue: 0.6312
  time to fit residues: 100.4343
Evaluate side-chains
  149 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  403 GLN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  200 GLU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  374 ASP
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 14 optimal weight:    0.3980
   chunk 125 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 147 optimal weight:    0.6980
   chunk 153 optimal weight:    6.9990
   chunk 99 optimal weight:    0.0060
   chunk 112 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    0.8198

-------------------------------------------------------------------------------
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 = 0.3254 r_free = 0.3254 target = 0.109279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.091181 restraints weight = 15728.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.81
r_work: 0.2870 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12906  Z= 0.111
  Angle     :  0.484  11.714  17556  Z= 0.252
  Chirality :  0.047   0.152   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.475  59.013   1735
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.74 %
    Favored  : 81.93 %
  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:  0.47 (0.21), residues: 1575
  helix:  0.30 (0.36), residues: 231
  sheet:  0.72 (0.24), residues: 462
  loop :  0.21 (0.21), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 404 
 TYR   0.013   0.001   TYR C 520 
 PHE   0.011   0.001   PHE A 199 
 TRP   0.005   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12906)
  covalent geometry    : angle       0.48369 (17556)
  hydrogen bonds       : bond        0.03153 (  420)
  hydrogen bonds       : angle       4.65672 ( 1251)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 118
  time to evaluate  : 0.512 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.7865 (tp30)
REVERT: A  166 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7702 (m-30)
REVERT: A  431 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8732 (pp)
REVERT: B   27 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8852 (mt0)
REVERT: B  113 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8427 (tt0)
REVERT: B  175 ASP cc_start: 0.8590 (m-30) cc_final: 0.8313 (m-30)
REVERT: B  205 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8070 (mm-30)
REVERT: B  220 LYS cc_start: 0.8223 (mptt) cc_final: 0.7950 (mptt)
REVERT: B  325 ASP cc_start: 0.7827 (p0) cc_final: 0.7566 (p0)
REVERT: C   74 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8467 (mt-10)
REVERT: C  220 LYS cc_start: 0.8334 (mppt) cc_final: 0.7906 (mmtp)
REVERT: C  308 GLU cc_start: 0.7820 (mp0) cc_final: 0.7589 (mp0)
REVERT: C  404 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7941 (ptp-110)
  outliers start: 34
  outliers final: 22
  residues processed: 147
  average time/residue: 0.6158
  time to fit residues: 98.2035
Evaluate side-chains
  147 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain A residue  309 SER
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  113 GLU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  200 GLU
Chi-restraints excluded: chain B residue  205 GLU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  309 SER
Chi-restraints excluded: chain B residue  378 ARG
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue   74 GLU
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  374 ASP
Chi-restraints excluded: chain C residue  482 THR
Chi-restraints excluded: chain C residue  502 LYS
Chi-restraints excluded: chain C residue  538 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 149 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0470
   chunk 14 optimal weight:    0.1980
   chunk 87 optimal weight:    5.9990
   chunk 109 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.8282

-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.109391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.091356 restraints weight = 15610.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.80
r_work: 0.2874 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12906  Z= 0.112
  Angle     :  0.492  12.710  17556  Z= 0.255
  Chirality :  0.047   0.144   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.438  59.919   1735
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.95 %
    Favored  : 81.93 %
  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:  0.49 (0.21), residues: 1575
  helix:  0.32 (0.36), residues: 231
  sheet:  0.72 (0.24), residues: 462
  loop :  0.23 (0.21), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 404 
 TYR   0.013   0.001   TYR C 520 
 PHE   0.011   0.001   PHE A 199 
 TRP   0.004   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 383 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12906)
  covalent geometry    : angle       0.49192 (17556)
  hydrogen bonds       : bond        0.03136 (  420)
  hydrogen bonds       : angle       4.61433 ( 1251)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3934.79 seconds
wall clock time: 67 minutes 46.22 seconds (4066.22 seconds total)