Starting phenix.real_space_refine
on Wed Jul 30 18:57:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfe_31950/07_2025/7vfe_31950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfe_31950/07_2025/7vfe_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_31950/07_2025/7vfe_31950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfe_31950/07_2025/7vfe_31950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfe_31950/07_2025/7vfe_31950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfe_31950/07_2025/7vfe_31950.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B
  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: 8.26, per 1000 atoms: 0.65
  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: 2.73
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.86
  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: 4.20

  Time building geometry restraints manager: 3.31 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.160
  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:          0.460
  Check model and map are aligned:         0.100
  Set scattering table:                    0.110
  Process input model:                     31.250
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.006   0.002   TRP A 108 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.016   0.002   PHE A  84 
 TYR   0.014   0.002   TYR A 463 
 ARG   0.004   0.001   ARG C 475 

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

*********************** 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  : 1.423 
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: 1.2218
  time to fit residues: 297.3798
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  : 1.605 
-------------------------------------------------------------------------------
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 131 optimal weight:    0.8980
   chunk 118 optimal weight:    0.1980
   chunk 65 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 141 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3263 r_free = 0.3263 target = 0.110239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.091781 restraints weight = 15330.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 1.81
r_work: 0.2861 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2718
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2718 r_free = 0.2718    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12906  Z= 0.114
  Angle     :  0.480   7.710  17556  Z= 0.256
  Chirality :  0.048   0.172   2025
  Planarity :  0.004   0.045   2241
  Dihedral  :  5.786  85.830   1754
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 13.62 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.20), residues: 1575
  helix: -0.32 (0.34), residues: 231
  sheet:  0.79 (0.24), residues: 438
  loop : -0.27 (0.19), residues: 906

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.003   0.001   HIS C 383 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.011   0.001   TYR C 520 
 ARG   0.002   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03793 (  420)
  hydrogen bonds       : angle       5.13038 ( 1251)
  covalent geometry    : bond        0.00256 (12906)
  covalent geometry    : angle       0.47995 (17556)

*********************** 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
  176 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 140
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.8877 (mtm) cc_final: 0.8670 (mtp)
REVERT: A  324 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.6113 (mp10)
REVERT: A  547 MET cc_start: 0.8152 (mmt) cc_final: 0.7794 (mmt)
REVERT: B  205 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7785 (mm-30)
REVERT: B  324 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.6113 (mp10)
REVERT: C   74 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8471 (mt-10)
REVERT: C  220 LYS cc_start: 0.8195 (mppt) cc_final: 0.7753 (mmtp)
REVERT: C  471 ASN cc_start: 0.8706 (m-40) cc_final: 0.8328 (m-40)
REVERT: C  524 GLN cc_start: 0.9156 (mt0) cc_final: 0.8852 (mt0)
  outliers start: 36
  outliers final: 18
  residues processed: 171
  average time/residue: 1.1949
  time to fit residues: 223.4885
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  : 1.514 
-------------------------------------------------------------------------------
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  324 GLN
Chi-restraints excluded: chain A residue  454 SER
Chi-restraints excluded: chain A residue  482 THR
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 62 optimal weight:    0.9980
   chunk 152 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   chunk 89 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 403 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 = 0.3234 r_free = 0.3234 target = 0.107983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.089489 restraints weight = 15656.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.81
r_work: 0.2834 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8774
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12906  Z= 0.167
  Angle     :  0.505   8.346  17556  Z= 0.266
  Chirality :  0.048   0.170   2025
  Planarity :  0.004   0.050   2241
  Dihedral  :  5.298  61.848   1744
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.24 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.20), residues: 1575
  helix:  0.10 (0.35), residues: 228
  sheet:  0.92 (0.24), residues: 438
  loop : -0.09 (0.20), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A 516 
 PHE   0.015   0.002   PHE C 199 
 TYR   0.014   0.002   TYR C 520 
 ARG   0.003   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  420)
  hydrogen bonds       : angle       4.98554 ( 1251)
  covalent geometry    : bond        0.00398 (12906)
  covalent geometry    : angle       0.50482 (17556)

*********************** 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
  164 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 1.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8512 (mt-10)
REVERT: A  113 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7866 (tp30)
REVERT: A  547 MET cc_start: 0.8202 (mmt) cc_final: 0.7934 (mmt)
REVERT: B   25 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7264 (m-30)
REVERT: B   27 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8736 (mt0)
REVERT: B  113 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8526 (tt0)
REVERT: B  205 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7981 (mm-30)
REVERT: B  325 ASP cc_start: 0.7505 (p0) cc_final: 0.7304 (p0)
REVERT: C   27 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8799 (mt0)
REVERT: C   74 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8399 (mt-10)
REVERT: C  220 LYS cc_start: 0.8303 (mppt) cc_final: 0.7874 (mmtp)
REVERT: C  378 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7641 (mtm180)
  outliers start: 39
  outliers final: 21
  residues processed: 158
  average time/residue: 1.6986
  time to fit residues: 291.2378
Evaluate side-chains
  149 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
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  147 THR
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  349 MET
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 148 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 105 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 139 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    2.7586

-------------------------------------------------------------------------------
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 = 0.3200 r_free = 0.3200 target = 0.105460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.086533 restraints weight = 15492.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 1.88
r_work: 0.2786 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  12906  Z= 0.279
  Angle     :  0.585   8.612  17556  Z= 0.307
  Chirality :  0.052   0.154   2025
  Planarity :  0.005   0.052   2241
  Dihedral  :  5.117  54.058   1738
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.24 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.20), residues: 1575
  helix: -0.04 (0.35), residues: 228
  sheet:  0.81 (0.25), residues: 432
  loop : -0.10 (0.19), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 108 
 HIS   0.006   0.002   HIS A 516 
 PHE   0.014   0.002   PHE C 199 
 TYR   0.016   0.002   TYR B 520 
 ARG   0.004   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04822 (  420)
  hydrogen bonds       : angle       5.20478 ( 1251)
  covalent geometry    : bond        0.00676 (12906)
  covalent geometry    : angle       0.58483 (17556)

*********************** 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
  168 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 120
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8560 (mt-10)
REVERT: A  113 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.7886 (tp30)
REVERT: B   25 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7393 (m-30)
REVERT: B   27 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8807 (mt0)
REVERT: B   33 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8525 (tpt)
REVERT: B  113 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8632 (tp30)
REVERT: B  205 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7998 (mm-30)
REVERT: B  325 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7542 (p0)
REVERT: C   74 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8534 (mt-10)
REVERT: C  220 LYS cc_start: 0.8332 (mppt) cc_final: 0.7839 (mmtp)
  outliers start: 48
  outliers final: 28
  residues processed: 155
  average time/residue: 1.3104
  time to fit residues: 221.3316
Evaluate side-chains
  154 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
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  120 ILE
Chi-restraints excluded: chain A residue  147 THR
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  245 THR
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  454 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   33 MET
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  325 ASP
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 97 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 146 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 113 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0370
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.3222 r_free = 0.3222 target = 0.107584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.088081 restraints weight = 15232.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.93
r_work: 0.2807 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2673 r_free = 0.2673    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12906  Z= 0.157
  Angle     :  0.501   8.980  17556  Z= 0.262
  Chirality :  0.048   0.143   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.819  55.055   1738
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.20), residues: 1575
  helix:  0.14 (0.35), residues: 228
  sheet:  0.79 (0.25), residues: 432
  loop :  0.05 (0.20), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.013   0.001   PHE C 199 
 TYR   0.012   0.001   TYR B 520 
 ARG   0.002   0.000   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  420)
  hydrogen bonds       : angle       4.92101 ( 1251)
  covalent geometry    : bond        0.00372 (12906)
  covalent geometry    : angle       0.50116 (17556)

*********************** 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
  164 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 1.690 
Fit side-chains
REVERT: A   74 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8484 (mt-10)
REVERT: A  113 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7911 (tp30)
REVERT: B   25 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7578 (m-30)
REVERT: B   27 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8751 (mt0)
REVERT: B  175 ASP cc_start: 0.8665 (m-30) cc_final: 0.8364 (m-30)
REVERT: B  205 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (mm-30)
REVERT: B  325 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7523 (p0)
REVERT: C   27 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8852 (mt0)
REVERT: C   74 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mt-10)
REVERT: C  220 LYS cc_start: 0.8300 (mppt) cc_final: 0.7830 (mmtp)
  outliers start: 41
  outliers final: 21
  residues processed: 157
  average time/residue: 1.3724
  time to fit residues: 234.7557
Evaluate side-chains
  148 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
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  120 ILE
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  482 THR
Chi-restraints excluded: chain B residue   25 ASP
Chi-restraints excluded: chain B residue   27 GLN
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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 113 optimal weight:    2.9990
   overall best weight:    1.6588

-------------------------------------------------------------------------------
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 = 0.3225 r_free = 0.3225 target = 0.107306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.089064 restraints weight = 15790.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.81
r_work: 0.2827 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12906  Z= 0.181
  Angle     :  0.521   9.854  17556  Z= 0.272
  Chirality :  0.048   0.145   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.813  55.490   1735
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.99 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.21), residues: 1575
  helix:  0.15 (0.35), residues: 228
  sheet:  0.70 (0.24), residues: 462
  loop :  0.02 (0.20), residues: 885

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  420)
  hydrogen bonds       : angle       4.94080 ( 1251)
  covalent geometry    : bond        0.00434 (12906)
  covalent geometry    : angle       0.52119 (17556)

*********************** 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
  163 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 118
  time to evaluate  : 1.591 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7869 (tm-30)
REVERT: A   74 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8517 (mt-10)
REVERT: A  113 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.7918 (tp30)
REVERT: B   25 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7425 (m-30)
REVERT: B   27 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8760 (mt0)
REVERT: B  113 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8520 (tt0)
REVERT: B  205 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8063 (mm-30)
REVERT: B  325 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (p0)
REVERT: C   27 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8827 (mt0)
REVERT: C   74 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (mt-10)
REVERT: C  127 LYS cc_start: 0.8938 (tptt) cc_final: 0.8664 (tptt)
REVERT: C  220 LYS cc_start: 0.8369 (mppt) cc_final: 0.7895 (mmtp)
  outliers start: 45
  outliers final: 26
  residues processed: 155
  average time/residue: 1.3272
  time to fit residues: 224.4776
Evaluate side-chains
  152 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
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  120 ILE
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  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  325 ASP
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  195 SER
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  398 SER
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 144 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 100 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 126 optimal weight:    0.1980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.108591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.090482 restraints weight = 15628.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.80
r_work: 0.2840 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2735 r_free = 0.2735    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12906  Z= 0.128
  Angle     :  0.493  10.653  17556  Z= 0.255
  Chirality :  0.047   0.139   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.614  56.602   1735
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.21), residues: 1575
  helix:  0.22 (0.36), residues: 231
  sheet:  0.70 (0.24), residues: 462
  loop :  0.09 (0.20), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.014   0.001   TYR C 520 
 ARG   0.005   0.000   ARG C 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  420)
  hydrogen bonds       : angle       4.78368 ( 1251)
  covalent geometry    : bond        0.00299 (12906)
  covalent geometry    : angle       0.49277 (17556)

*********************** 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
  162 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 1.427 
Fit side-chains
REVERT: A   35 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7928 (tm-30)
REVERT: A   74 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8501 (mt-10)
REVERT: A  113 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.7859 (tp30)
REVERT: B   25 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7494 (m-30)
REVERT: B   27 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8834 (mt0)
REVERT: B  113 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8459 (tt0)
REVERT: B  175 ASP cc_start: 0.8566 (m-30) cc_final: 0.8286 (m-30)
REVERT: B  205 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8069 (mm-30)
REVERT: C   74 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8479 (mt-10)
REVERT: C  127 LYS cc_start: 0.8921 (tptt) cc_final: 0.8602 (tptt)
REVERT: C  220 LYS cc_start: 0.8342 (mppt) cc_final: 0.7889 (mmtp)
  outliers start: 42
  outliers final: 28
  residues processed: 154
  average time/residue: 1.2574
  time to fit residues: 210.9690
Evaluate side-chains
  154 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
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  120 ILE
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  349 MET
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  454 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  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   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  398 SER
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 45 optimal weight:    6.9990
   chunk 69 optimal weight:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 99 optimal weight:    0.0010
   overall best weight:    0.4186

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.110567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.092520 restraints weight = 15797.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.81
r_work: 0.2890 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2766 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.97   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12906  Z= 0.084
  Angle     :  0.464  11.685  17556  Z= 0.239
  Chirality :  0.046   0.127   2025
  Planarity :  0.004   0.050   2241
  Dihedral  :  4.305  59.611   1735
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.21), residues: 1575
  helix:  0.35 (0.36), residues: 231
  sheet:  0.80 (0.23), residues: 468
  loop :  0.17 (0.21), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 108 
 HIS   0.002   0.000   HIS A 383 
 PHE   0.012   0.001   PHE C 357 
 TYR   0.010   0.001   TYR C 520 
 ARG   0.011   0.000   ARG C 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02766 (  420)
  hydrogen bonds       : angle       4.49994 ( 1251)
  covalent geometry    : bond        0.00189 (12906)
  covalent geometry    : angle       0.46416 (17556)

*********************** 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
  159 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.529 
Fit side-chains
REVERT: A  220 LYS cc_start: 0.8398 (mppt) cc_final: 0.7882 (mmtp)
REVERT: B  113 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8392 (tt0)
REVERT: B  175 ASP cc_start: 0.8601 (m-30) cc_final: 0.8309 (m-30)
REVERT: B  205 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (pt0)
REVERT: B  325 ASP cc_start: 0.7873 (p0) cc_final: 0.7647 (p0)
REVERT: C  127 LYS cc_start: 0.8896 (tptt) cc_final: 0.8577 (tptt)
REVERT: C  220 LYS cc_start: 0.8239 (mppt) cc_final: 0.7830 (mmtp)
REVERT: C  404 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7932 (ptp-110)
REVERT: C  471 ASN cc_start: 0.8669 (m-40) cc_final: 0.8326 (m-40)
  outliers start: 32
  outliers final: 20
  residues processed: 154
  average time/residue: 1.3630
  time to fit residues: 228.8300
Evaluate side-chains
  141 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
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  398 SER
Chi-restraints excluded: chain A residue  482 THR
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  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
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 127 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 128 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 139 optimal weight:    5.9990
   chunk 119 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 140 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.108560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.090405 restraints weight = 15624.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.80
r_work: 0.2834 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2714
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2714 r_free = 0.2714    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 = 0.2714 r_free = 0.2714    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2714
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12906  Z= 0.150
  Angle     :  0.512  10.966  17556  Z= 0.264
  Chirality :  0.047   0.133   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.558  59.860   1735
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.29 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.21), residues: 1575
  helix:  0.34 (0.36), residues: 231
  sheet:  0.74 (0.24), residues: 462
  loop :  0.17 (0.21), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 250 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.014   0.001   TYR C 520 
 ARG   0.009   0.000   ARG C 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03505 (  420)
  hydrogen bonds       : angle       4.72520 ( 1251)
  covalent geometry    : bond        0.00354 (12906)
  covalent geometry    : angle       0.51247 (17556)

*********************** 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
  145 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 1.530 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.7866 (tp30)
REVERT: A  245 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8819 (m)
REVERT: B  113 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8512 (tt0)
REVERT: B  175 ASP cc_start: 0.8568 (m-30) cc_final: 0.8288 (m-30)
REVERT: B  205 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8123 (pt0)
REVERT: C  220 LYS cc_start: 0.8325 (mppt) cc_final: 0.7887 (mmtp)
REVERT: C  404 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7960 (ptp-110)
  outliers start: 28
  outliers final: 22
  residues processed: 143
  average time/residue: 1.3349
  time to fit residues: 208.4377
Evaluate side-chains
  143 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 1.600 
-------------------------------------------------------------------------------
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  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  454 SER
Chi-restraints excluded: chain A residue  482 THR
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  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  195 SER
Chi-restraints excluded: chain C residue  246 VAL
Chi-restraints excluded: chain C residue  309 SER
Chi-restraints excluded: chain C residue  398 SER
Chi-restraints excluded: chain C residue  482 THR
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 108 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 121 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.109688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.091601 restraints weight = 15509.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.80
r_work: 0.2882 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12906  Z= 0.108
  Angle     :  0.493  11.661  17556  Z= 0.254
  Chirality :  0.046   0.128   2025
  Planarity :  0.004   0.051   2241
  Dihedral  :  4.406  58.815   1735
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.29 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.21), residues: 1575
  helix:  0.34 (0.36), residues: 231
  sheet:  0.75 (0.24), residues: 462
  loop :  0.20 (0.21), residues: 882

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 108 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.011   0.001   PHE A 199 
 TYR   0.013   0.001   TYR C 520 
 ARG   0.009   0.000   ARG C 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03091 (  420)
  hydrogen bonds       : angle       4.60804 ( 1251)
  covalent geometry    : bond        0.00248 (12906)
  covalent geometry    : angle       0.49326 (17556)

********************** 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
  145 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 1.531 
Fit side-chains
REVERT: A  113 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.7864 (tp30)
REVERT: A  245 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8808 (m)
REVERT: B  113 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8415 (tt0)
REVERT: B  175 ASP cc_start: 0.8597 (m-30) cc_final: 0.8303 (m-30)
REVERT: B  205 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8122 (pt0)
REVERT: C  220 LYS cc_start: 0.8319 (mppt) cc_final: 0.7906 (mmtp)
REVERT: C  308 GLU cc_start: 0.7823 (mp0) cc_final: 0.7614 (mp0)
REVERT: C  404 ARG cc_start: 0.8195 (mtm110) cc_final: 0.7992 (ptp-110)
  outliers start: 28
  outliers final: 19
  residues processed: 141
  average time/residue: 1.3243
  time to fit residues: 203.3414
Evaluate side-chains
  140 residues out of total 1461 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 1.501 
-------------------------------------------------------------------------------
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  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  482 THR
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  485 ILE
Chi-restraints excluded: chain B residue  502 LYS
Chi-restraints excluded: chain B residue  538 ASP
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
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 6 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3226 r_free = 0.3226 target = 0.107354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.089169 restraints weight = 15609.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 1.80
r_work: 0.2821 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12906  Z= 0.206
  Angle     :  0.559  12.621  17556  Z= 0.290
  Chirality :  0.049   0.134   2025
  Planarity :  0.004   0.052   2241
  Dihedral  :  4.757  58.080   1735
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.22 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.21), residues: 1575
  helix:  0.25 (0.36), residues: 228
  sheet:  0.74 (0.24), residues: 462
  loop :  0.13 (0.20), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A 516 
 PHE   0.015   0.002   PHE C 357 
 TYR   0.017   0.002   TYR C 520 
 ARG   0.008   0.000   ARG C 404 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  420)
  hydrogen bonds       : angle       4.88922 ( 1251)
  covalent geometry    : bond        0.00494 (12906)
  covalent geometry    : angle       0.55853 (17556)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8835.32 seconds
wall clock time: 155 minutes 33.50 seconds (9333.50 seconds total)