Starting phenix.real_space_refine
on Thu Feb 13 19:57:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x2l_22011/02_2025/6x2l_22011.cif"
  }
  resolution = 2.85
  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=   0.004
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      69      5.16       5
     C    6159      2.51       5
     N    1491      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9396
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 411, 3132
          Classifications: {'peptide': 411}
          Link IDs: {'PTRANS': 11, 'TRANS': 399}
          Chain breaks: 2
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 5.83, per 1000 atoms: 0.62
  Number of scatterers: 9396
  At special positions: 0
  Unit cell: (113.984, 109.824, 82.368, 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      69     16.00
     O    1677      8.00
     N    1491      7.00
     C    6159      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: 2.26
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2280

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      81.3% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.613A  pdb=" N   ALA A  27 " --> pdb=" O   SER A  23 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG A  39 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.739A  pdb=" N   ALA A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 86
      removed outlier: 3.580A  pdb=" N   LEU A  59 " --> pdb=" O   PRO A  55 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A  66 " --> pdb=" O   MET A  62 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LEU A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 3.761A  pdb=" N   SER A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 117
      removed outlier: 3.565A  pdb=" N   VAL A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.554A  pdb=" N   MET A 142 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 211 through 230
      removed outlier: 3.517A  pdb=" N   GLY A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLY A 230 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 273
      Proline residue:  A 259  - end of helix
      removed outlier: 3.631A  pdb=" N   PHE A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 299
      removed outlier: 3.679A  pdb=" N   THR A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 309
      removed outlier: 3.623A  pdb=" N   VAL A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 319
      removed outlier: 3.608A  pdb=" N   PHE A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
      removed outlier: 3.548A  pdb=" N   THR A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 349
      removed outlier: 4.158A  pdb=" N   ARG A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASN A 347 " --> pdb=" O   CYS A 343 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 363
      removed outlier: 4.179A  pdb=" N   PHE A 357 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 367 through 385
      removed outlier: 3.595A  pdb=" N   VAL A 379 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 401
      removed outlier: 3.696A  pdb=" N   THR A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.527A  pdb=" N   SER A 405 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 3.592A  pdb=" N   MET A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL A 426 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.995A  pdb=" N   ILE A 436 " --> pdb=" O   ASP A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 466
      removed outlier: 3.594A  pdb=" N   LEU A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG A 445 " --> pdb=" O   TRP A 441 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   PHE A 446 " --> pdb=" O   LEU A 442 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   MET A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP A 455 " --> pdb=" O   ASN A 451 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS A 464 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 40
      removed outlier: 3.613A  pdb=" N   ALA B  27 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG B  39 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU B  40 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 53
      removed outlier: 3.739A  pdb=" N   ALA B  53 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 86
      removed outlier: 3.580A  pdb=" N   LEU B  59 " --> pdb=" O   PRO B  55 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B  67 " --> pdb=" O   LEU B  63 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LEU B  68 " --> pdb=" O   LYS B  64 " (cutoff:3.500A)
      Proline residue:  B  69  - end of helix
      removed outlier: 3.761A  pdb=" N   SER B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 117
      removed outlier: 3.565A  pdb=" N   VAL B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 150
      removed outlier: 3.554A  pdb=" N   MET B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE B 146 " --> pdb=" O   MET B 142 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE B 150 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 158
    Processing helix  chain 'B' and resid 211 through 230
      removed outlier: 3.518A  pdb=" N   GLY B 227 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLY B 230 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 273
      Proline residue:  B 259  - end of helix
      removed outlier: 3.631A  pdb=" N   PHE B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 277 through 299
      removed outlier: 3.679A  pdb=" N   THR B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 309
      removed outlier: 3.624A  pdb=" N   VAL B 308 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 319
      removed outlier: 3.608A  pdb=" N   PHE B 316 " --> pdb=" O   ASN B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
      removed outlier: 3.549A  pdb=" N   THR B 326 " --> pdb=" O   GLN B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 349
      removed outlier: 4.158A  pdb=" N   ARG B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASN B 347 " --> pdb=" O   CYS B 343 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN B 349 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 363
      removed outlier: 4.179A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      Proline residue:  B 360  - end of helix
    Processing helix  chain 'B' and resid 367 through 385
      removed outlier: 3.595A  pdb=" N   VAL B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 401
      removed outlier: 3.696A  pdb=" N   THR B 396 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 406
      removed outlier: 3.528A  pdb=" N   SER B 405 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 427
      removed outlier: 3.592A  pdb=" N   MET B 419 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL B 426 " --> pdb=" O   VAL B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 431
      No H-bonds generated for 'chain 'B' and resid 429 through 431'
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 3.994A  pdb=" N   ILE B 436 " --> pdb=" O   ASP B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 466
      removed outlier: 3.595A  pdb=" N   LEU B 443 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG B 445 " --> pdb=" O   TRP B 441 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   PHE B 446 " --> pdb=" O   LEU B 442 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   MET B 449 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 455 " --> pdb=" O   ASN B 451 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY B 460 " --> pdb=" O   ALA B 456 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B 464 " --> pdb=" O   GLY B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 40
      removed outlier: 3.613A  pdb=" N   ALA C  27 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG C  39 " --> pdb=" O   GLY C  35 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLU C  40 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 53
      removed outlier: 3.739A  pdb=" N   ALA C  53 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 86
      removed outlier: 3.579A  pdb=" N   LEU C  59 " --> pdb=" O   PRO C  55 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS C  64 " --> pdb=" O   MET C  60 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE C  66 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LEU C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      Proline residue:  C  69  - end of helix
      removed outlier: 3.762A  pdb=" N   SER C  84 " --> pdb=" O   ALA C  80 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL C  86 " --> pdb=" O   LEU C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 117
      removed outlier: 3.565A  pdb=" N   VAL C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 150
      removed outlier: 3.555A  pdb=" N   MET C 142 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE C 146 " --> pdb=" O   MET C 142 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE C 150 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 158
    Processing helix  chain 'C' and resid 211 through 230
      removed outlier: 3.518A  pdb=" N   GLY C 227 " --> pdb=" O   GLY C 223 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLY C 230 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 273
      Proline residue:  C 259  - end of helix
      removed outlier: 3.631A  pdb=" N   PHE C 264 " --> pdb=" O   LEU C 260 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLU C 272 " --> pdb=" O   GLY C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 277 through 299
      removed outlier: 3.678A  pdb=" N   THR C 291 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 300 through 309
      removed outlier: 3.622A  pdb=" N   VAL C 308 " --> pdb=" O   ILE C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 319
      removed outlier: 3.608A  pdb=" N   PHE C 316 " --> pdb=" O   ASN C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 320 through 330
      removed outlier: 3.548A  pdb=" N   THR C 326 " --> pdb=" O   GLN C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 349
      removed outlier: 4.158A  pdb=" N   ARG C 342 " --> pdb=" O   PRO C 338 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASN C 347 " --> pdb=" O   CYS C 343 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLN C 349 " --> pdb=" O   GLU C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 363
      removed outlier: 4.179A  pdb=" N   PHE C 357 " --> pdb=" O   ARG C 353 " (cutoff:3.500A)
      Proline residue:  C 360  - end of helix
    Processing helix  chain 'C' and resid 367 through 385
      removed outlier: 3.595A  pdb=" N   VAL C 379 " --> pdb=" O   ALA C 375 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 401
      removed outlier: 3.696A  pdb=" N   THR C 396 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 406
      removed outlier: 3.527A  pdb=" N   SER C 405 " --> pdb=" O   THR C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 427
      removed outlier: 3.592A  pdb=" N   MET C 419 " --> pdb=" O   GLY C 415 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL C 426 " --> pdb=" O   VAL C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 432
      removed outlier: 3.589A  pdb=" N   ASP C 432 " --> pdb=" O   PRO C 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 429 through 432'
    Processing helix  chain 'C' and resid 433 through 438
    Processing helix  chain 'C' and resid 439 through 466
      removed outlier: 3.594A  pdb=" N   LEU C 443 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG C 445 " --> pdb=" O   TRP C 441 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   PHE C 446 " --> pdb=" O   LEU C 442 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   MET C 449 " --> pdb=" O   ARG C 445 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP C 455 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR C 459 " --> pdb=" O   ASP C 455 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLY C 460 " --> pdb=" O   ALA C 456 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LYS C 464 " --> pdb=" O   GLY C 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167
    Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161
    Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167
    Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161
    Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167

    624 hydrogen bonds defined for protein.
    1836 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1670
        1.32 -     1.45: 2168
        1.45 -     1.57: 5573
        1.57 -     1.70: 0
        1.70 -     1.82: 123
  Bond restraints: 9534
  Sorted by residual:
  bond pdb=" C   MET C 419 "
       pdb=" O   MET C 419 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.037 1.19e-02 7.06e+03 9.55e+00
  bond pdb=" C   MET A 419 "
       pdb=" O   MET A 419 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.036 1.19e-02 7.06e+03 9.28e+00
  bond pdb=" C   MET B 419 "
       pdb=" O   MET B 419 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 1.19e-02 7.06e+03 9.09e+00
  bond pdb=" N   LEU B 372 "
       pdb=" CA  LEU B 372 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.41e+00
  bond pdb=" N   LEU A 372 "
       pdb=" CA  LEU A 372 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.20e+00
  ... (remaining 9529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 12242
        1.89 -     3.77: 591
        3.77 -     5.66: 73
        5.66 -     7.55: 18
        7.55 -     9.44: 12
  Bond angle restraints: 12936
  Sorted by residual:
  angle pdb=" C   ASP C 388 "
        pdb=" N   LEU C 389 "
        pdb=" CA  LEU C 389 "
      ideal   model   delta    sigma   weight residual
     121.54  128.88   -7.34 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" C   ASP A 388 "
        pdb=" N   LEU A 389 "
        pdb=" CA  LEU A 389 "
      ideal   model   delta    sigma   weight residual
     121.54  128.87   -7.33 1.91e+00 2.74e-01 1.47e+01
  angle pdb=" C   ASP B 388 "
        pdb=" N   LEU B 389 "
        pdb=" CA  LEU B 389 "
      ideal   model   delta    sigma   weight residual
     121.54  128.84   -7.30 1.91e+00 2.74e-01 1.46e+01
  angle pdb=" CB  MET C 473 "
        pdb=" CG  MET C 473 "
        pdb=" SD  MET C 473 "
      ideal   model   delta    sigma   weight residual
     112.70  103.26    9.44 3.00e+00 1.11e-01 9.89e+00
  angle pdb=" CB  MET A 473 "
        pdb=" CG  MET A 473 "
        pdb=" SD  MET A 473 "
      ideal   model   delta    sigma   weight residual
     112.70  103.30    9.40 3.00e+00 1.11e-01 9.82e+00
  ... (remaining 12931 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.78: 5150
       16.78 -    33.56: 430
       33.56 -    50.35: 96
       50.35 -    67.13: 21
       67.13 -    83.91: 9
  Dihedral angle restraints: 5706
    sinusoidal: 2172
      harmonic: 3534
  Sorted by residual:
  dihedral pdb=" CA  LEU A 384 "
           pdb=" C   LEU A 384 "
           pdb=" N   ASN A 385 "
           pdb=" CA  ASN A 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.52   19.48     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  LEU C 384 "
           pdb=" C   LEU C 384 "
           pdb=" N   ASN C 385 "
           pdb=" CA  ASN C 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.53   19.47     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  LEU B 384 "
           pdb=" C   LEU B 384 "
           pdb=" N   ASN B 385 "
           pdb=" CA  ASN B 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.54   19.46     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 5703 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 847
       0.039 -    0.077: 565
       0.077 -    0.116: 154
       0.116 -    0.154: 59
       0.154 -    0.193: 19
  Chirality restraints: 1644
  Sorted by residual:
  chirality pdb=" CB  VAL C 433 "
            pdb=" CA  VAL C 433 "
            pdb=" CG1 VAL C 433 "
            pdb=" CG2 VAL C 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" CB  VAL B 433 "
            pdb=" CA  VAL B 433 "
            pdb=" CG1 VAL B 433 "
            pdb=" CG2 VAL B 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.04e-01
  chirality pdb=" CB  VAL A 433 "
            pdb=" CA  VAL A 433 "
            pdb=" CG1 VAL A 433 "
            pdb=" CG2 VAL A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.92e-01
  ... (remaining 1641 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 301 "   -0.049 5.00e-02 4.00e+02   7.26e-02 8.43e+00
        pdb=" N   PRO C 302 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO C 302 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 302 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 301 "   -0.049 5.00e-02 4.00e+02   7.25e-02 8.40e+00
        pdb=" N   PRO B 302 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 302 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 302 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 301 "   -0.049 5.00e-02 4.00e+02   7.25e-02 8.40e+00
        pdb=" N   PRO A 302 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 302 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 302 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 60
        2.64 -     3.21: 8450
        3.21 -     3.77: 14468
        3.77 -     4.34: 20729
        4.34 -     4.90: 33676
  Nonbonded interactions: 77383
  Sorted by model distance:
  nonbonded pdb=" N   GLN B 413 "
            pdb=" OE1 GLN B 413 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" N   GLN A 413 "
            pdb=" OE1 GLN A 413 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" N   GLN C 413 "
            pdb=" OE1 GLN C 413 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" O   SER A 331 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER B 331 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.339 3.040
  ... (remaining 77378 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.270
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
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      :  0.009   0.075   9534  Z= 0.585
  Angle     :  0.960   9.435  12936  Z= 0.513
  Chirality :  0.056   0.193   1644
  Planarity :  0.007   0.073   1572
  Dihedral  : 13.682  83.912   3426
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  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: -6.46 (0.14), residues: 1215
  helix: -4.23 (0.07), residues: 975
  sheet: -2.87 (0.80), residues: 54
  loop : -2.72 (0.35), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 276 
 HIS   0.003   0.001   HIS B  41 
 PHE   0.021   0.003   PHE B 341 
 TYR   0.020   0.003   TYR C 373 
 ARG   0.006   0.001   ARG B 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A   93 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7933 (mtm-85)
REVERT: A  200 TYR cc_start: 0.8079 (m-80) cc_final: 0.7821 (m-80)
REVERT: A  322 GLN cc_start: 0.8018 (tp40) cc_final: 0.7739 (mm-40)
REVERT: A  352 LYS cc_start: 0.8364 (tmtm) cc_final: 0.7721 (mtmt)
REVERT: A  393 GLN cc_start: 0.8605 (mt0) cc_final: 0.8184 (mt0)
REVERT: B  200 TYR cc_start: 0.8220 (m-80) cc_final: 0.7731 (m-10)
REVERT: B  248 MET cc_start: 0.8289 (tpp) cc_final: 0.8083 (tpt)
REVERT: B  280 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7807 (tmm160)
REVERT: C  200 TYR cc_start: 0.8208 (m-80) cc_final: 0.7746 (m-10)
REVERT: C  248 MET cc_start: 0.8260 (tpp) cc_final: 0.8023 (mmt)
REVERT: C  316 PHE cc_start: 0.8052 (t80) cc_final: 0.7805 (t80)
REVERT: C  322 GLN cc_start: 0.8040 (tp40) cc_final: 0.7667 (mm110)
  outliers start: 0
  outliers final: 2
  residues processed: 200
  average time/residue: 1.2973
  time to fit residues: 276.2509
Evaluate side-chains
  148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 146
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain C residue  461 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0170
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
B  85 ASN
C  85 ASN
C 156 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.100592 restraints weight = 11132.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.83
r_work: 0.2925 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9534  Z= 0.167
  Angle     :  0.559   8.084  12936  Z= 0.292
  Chirality :  0.038   0.130   1644
  Planarity :  0.005   0.037   1572
  Dihedral  :  4.546  18.591   1297
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.34 %
    Favored  : 87.92 %
  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: -2.96 (0.20), residues: 1215
  helix: -1.59 (0.14), residues: 960
  sheet: -3.04 (0.69), residues: 54
  loop : -2.34 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 441 
 HIS   0.001   0.000   HIS B 296 
 PHE   0.015   0.002   PHE B 218 
 TYR   0.010   0.001   TYR B 373 
 ARG   0.005   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7830 (tp30)
REVERT: A  248 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8869 (mmt)
REVERT: A  322 GLN cc_start: 0.7981 (tp40) cc_final: 0.7454 (mm-40)
REVERT: A  329 MET cc_start: 0.6417 (mmm) cc_final: 0.5897 (mtt)
REVERT: A  431 GLU cc_start: 0.7427 (pm20) cc_final: 0.7111 (mp0)
REVERT: B  200 TYR cc_start: 0.8282 (m-80) cc_final: 0.7899 (m-10)
REVERT: B  248 MET cc_start: 0.8986 (tpp) cc_final: 0.8744 (mmm)
REVERT: B  473 MET cc_start: 0.6742 (ttt) cc_final: 0.6394 (mtp)
REVERT: C  248 MET cc_start: 0.9062 (tpp) cc_final: 0.8624 (mmt)
REVERT: C  280 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6922 (ttm170)
REVERT: C  322 GLN cc_start: 0.7938 (tp40) cc_final: 0.7426 (mm-40)
REVERT: C  393 GLN cc_start: 0.8714 (mt0) cc_final: 0.8488 (mt0)
  outliers start: 18
  outliers final: 6
  residues processed: 188
  average time/residue: 1.0729
  time to fit residues: 217.7065
Evaluate side-chains
  149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  426 VAL
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  373 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 120 optimal weight:    0.8980
   chunk 82 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 156 GLN
B  85 ASN
B 312 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.094481 restraints weight = 11189.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 1.90
r_work: 0.2834 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9534  Z= 0.308
  Angle     :  0.581   6.909  12936  Z= 0.298
  Chirality :  0.041   0.126   1644
  Planarity :  0.004   0.035   1572
  Dihedral  :  4.335  18.827   1293
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 13.62 %
    Favored  : 83.29 %
  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: -1.34 (0.23), residues: 1215
  helix: -0.34 (0.16), residues: 963
  sheet: -2.57 (0.70), residues: 54
  loop : -2.44 (0.38), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  19 
 HIS   0.001   0.001   HIS A  41 
 PHE   0.017   0.002   PHE A 218 
 TYR   0.007   0.001   TYR B 373 
 ARG   0.004   0.001   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 154
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7773 (tp30)
REVERT: A  205 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7406 (tmm)
REVERT: A  276 TRP cc_start: 0.7479 (m100) cc_final: 0.7114 (m-90)
REVERT: A  393 GLN cc_start: 0.8630 (mt0) cc_final: 0.8142 (mt0)
REVERT: A  431 GLU cc_start: 0.7356 (pm20) cc_final: 0.7034 (mp0)
REVERT: B   75 MET cc_start: 0.9205 (mmm) cc_final: 0.8871 (tpp)
REVERT: B  200 TYR cc_start: 0.8345 (m-80) cc_final: 0.7950 (m-10)
REVERT: B  248 MET cc_start: 0.8994 (tpp) cc_final: 0.8719 (mmm)
REVERT: B  468 LYS cc_start: 0.7083 (mttm) cc_final: 0.6869 (mttm)
REVERT: B  473 MET cc_start: 0.6638 (ttt) cc_final: 0.6329 (mtp)
REVERT: C  248 MET cc_start: 0.9071 (tpp) cc_final: 0.8593 (mmt)
REVERT: C  316 PHE cc_start: 0.7725 (t80) cc_final: 0.7519 (t80)
REVERT: C  322 GLN cc_start: 0.7996 (tp40) cc_final: 0.7498 (mm-40)
  outliers start: 32
  outliers final: 14
  residues processed: 169
  average time/residue: 1.1737
  time to fit residues: 213.2918
Evaluate side-chains
  156 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  373 TYR
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  411 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 78 optimal weight:    0.0030
   chunk 91 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 97 optimal weight:    0.6980
   chunk 88 optimal weight:    0.6980
   chunk 84 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B  85 ASN
B 393 GLN
C  85 ASN
C 312 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.101044 restraints weight = 11170.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.84
r_work: 0.2948 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9534  Z= 0.142
  Angle     :  0.487   6.406  12936  Z= 0.250
  Chirality :  0.038   0.127   1644
  Planarity :  0.003   0.028   1572
  Dihedral  :  3.890  17.640   1293
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.46 %
    Favored  : 81.84 %
  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:  0.04 (0.24), residues: 1215
  helix:  0.56 (0.17), residues: 981
  sheet: -2.39 (0.70), residues: 54
  loop : -1.62 (0.43), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 441 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.012   0.001   PHE A 218 
 TYR   0.009   0.001   TYR A 373 
 ARG   0.003   0.000   ARG A 315 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A  248 MET cc_start: 0.9084 (tpt) cc_final: 0.8880 (mmp)
REVERT: A  342 ARG cc_start: 0.7040 (ppt170) cc_final: 0.6807 (ppt90)
REVERT: A  393 GLN cc_start: 0.8644 (mt0) cc_final: 0.8181 (mt0)
REVERT: A  431 GLU cc_start: 0.7418 (pm20) cc_final: 0.7090 (mp0)
REVERT: B   75 MET cc_start: 0.9150 (mmm) cc_final: 0.8800 (tpp)
REVERT: B  200 TYR cc_start: 0.8351 (m-80) cc_final: 0.7989 (m-10)
REVERT: B  248 MET cc_start: 0.8985 (tpp) cc_final: 0.8738 (mmm)
REVERT: B  258 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8458 (ttm)
REVERT: B  303 LEU cc_start: 0.8214 (tp) cc_final: 0.7799 (tt)
REVERT: B  473 MET cc_start: 0.6704 (ttt) cc_final: 0.6393 (mtp)
REVERT: C  205 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.7017 (tmm)
REVERT: C  248 MET cc_start: 0.9041 (tpp) cc_final: 0.8583 (mmt)
REVERT: C  280 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6820 (ttm170)
REVERT: C  303 LEU cc_start: 0.8248 (tp) cc_final: 0.7858 (tt)
REVERT: C  322 GLN cc_start: 0.7897 (tp40) cc_final: 0.7350 (mm-40)
REVERT: C  342 ARG cc_start: 0.7336 (ppt170) cc_final: 0.7069 (ppt90)
REVERT: C  351 ASP cc_start: 0.7009 (t0) cc_final: 0.6706 (t0)
REVERT: C  463 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7501 (tm-30)
  outliers start: 28
  outliers final: 12
  residues processed: 179
  average time/residue: 1.1804
  time to fit residues: 226.7065
Evaluate side-chains
  164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  366 ASN
Chi-restraints excluded: chain B residue  373 TYR
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 115 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B  85 ASN
B 393 GLN
C  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.099346 restraints weight = 11135.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.73
r_work: 0.2853 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9534  Z= 0.257
  Angle     :  0.541   6.030  12936  Z= 0.275
  Chirality :  0.040   0.130   1644
  Planarity :  0.003   0.036   1572
  Dihedral  :  4.008  17.627   1293
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.14 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.27 (0.24), residues: 1215
  helix:  0.77 (0.17), residues: 969
  sheet: -2.19 (0.73), residues: 54
  loop : -1.73 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  19 
 HIS   0.001   0.001   HIS C 296 
 PHE   0.016   0.002   PHE A 218 
 TYR   0.008   0.001   TYR C 373 
 ARG   0.003   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 1.132 
Fit side-chains
REVERT: A  275 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8040 (m-30)
REVERT: A  276 TRP cc_start: 0.7469 (m100) cc_final: 0.7128 (m-90)
REVERT: A  342 ARG cc_start: 0.7157 (ppt170) cc_final: 0.6857 (ppt90)
REVERT: A  393 GLN cc_start: 0.8672 (mt0) cc_final: 0.8181 (mt0)
REVERT: A  431 GLU cc_start: 0.7429 (pm20) cc_final: 0.7111 (mp0)
REVERT: A  463 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7488 (tm-30)
REVERT: B   75 MET cc_start: 0.9168 (mmm) cc_final: 0.8830 (tpp)
REVERT: B  200 TYR cc_start: 0.8387 (m-80) cc_final: 0.8042 (m-10)
REVERT: B  248 MET cc_start: 0.9026 (tpp) cc_final: 0.8768 (mmm)
REVERT: B  320 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7475 (mmt)
REVERT: B  366 ASN cc_start: 0.8214 (t0) cc_final: 0.7994 (t0)
REVERT: B  463 GLU cc_start: 0.7864 (tt0) cc_final: 0.7326 (tm-30)
REVERT: B  473 MET cc_start: 0.6710 (ttt) cc_final: 0.6390 (mtp)
REVERT: C  248 MET cc_start: 0.9082 (tpp) cc_final: 0.8604 (mmt)
REVERT: C  280 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6888 (ttm170)
REVERT: C  322 GLN cc_start: 0.7904 (tp40) cc_final: 0.7389 (mm-40)
REVERT: C  342 ARG cc_start: 0.7383 (ppt170) cc_final: 0.7085 (ppt90)
REVERT: C  351 ASP cc_start: 0.7069 (t0) cc_final: 0.6758 (t0)
REVERT: C  393 GLN cc_start: 0.8720 (mt0) cc_final: 0.8440 (mt0)
REVERT: C  463 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7560 (tm-30)
  outliers start: 34
  outliers final: 18
  residues processed: 164
  average time/residue: 1.2152
  time to fit residues: 214.0635
Evaluate side-chains
  166 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  373 TYR
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 116 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 393 GLN
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.137919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.097379 restraints weight = 11075.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.81
r_work: 0.2853 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9534  Z= 0.231
  Angle     :  0.522   5.753  12936  Z= 0.266
  Chirality :  0.039   0.126   1644
  Planarity :  0.003   0.035   1572
  Dihedral  :  3.975  17.549   1293
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.23 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1215
  helix:  0.88 (0.17), residues: 987
  sheet: -1.99 (0.74), residues: 54
  loop : -1.86 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  19 
 HIS   0.001   0.000   HIS C 296 
 PHE   0.015   0.002   PHE A 218 
 TYR   0.010   0.001   TYR A 373 
 ARG   0.002   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  322 GLN cc_start: 0.7916 (tp40) cc_final: 0.7389 (mm-40)
REVERT: A  342 ARG cc_start: 0.7128 (ppt170) cc_final: 0.6907 (ppt90)
REVERT: A  393 GLN cc_start: 0.8688 (mt0) cc_final: 0.8173 (mt0)
REVERT: A  431 GLU cc_start: 0.7436 (pm20) cc_final: 0.7181 (mp0)
REVERT: A  463 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: B   75 MET cc_start: 0.9182 (mmm) cc_final: 0.8846 (tpp)
REVERT: B  200 TYR cc_start: 0.8376 (m-80) cc_final: 0.8001 (m-10)
REVERT: B  248 MET cc_start: 0.9032 (tpp) cc_final: 0.8788 (mmm)
REVERT: B  342 ARG cc_start: 0.7491 (ppt170) cc_final: 0.7134 (ppt90)
REVERT: B  463 GLU cc_start: 0.7915 (tt0) cc_final: 0.7376 (tm-30)
REVERT: B  473 MET cc_start: 0.6698 (ttt) cc_final: 0.6380 (mtp)
REVERT: C  248 MET cc_start: 0.9100 (tpp) cc_final: 0.8631 (mmt)
REVERT: C  280 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6869 (ttm170)
REVERT: C  320 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7275 (mmt)
REVERT: C  322 GLN cc_start: 0.7879 (tp40) cc_final: 0.7402 (mm-40)
REVERT: C  342 ARG cc_start: 0.7374 (ppt170) cc_final: 0.7048 (ppt90)
REVERT: C  351 ASP cc_start: 0.7113 (t0) cc_final: 0.6743 (t0)
REVERT: C  463 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7529 (tm-30)
  outliers start: 33
  outliers final: 17
  residues processed: 165
  average time/residue: 1.2570
  time to fit residues: 221.6822
Evaluate side-chains
  162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain C residue  320 MET
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 99 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0570
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 393 GLN
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.099032 restraints weight = 11259.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.86
r_work: 0.2905 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9534  Z= 0.139
  Angle     :  0.482   5.363  12936  Z= 0.247
  Chirality :  0.037   0.123   1644
  Planarity :  0.003   0.029   1572
  Dihedral  :  3.727  18.031   1293
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.68 %
    Favored  : 79.61 %
  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:  1.03 (0.25), residues: 1215
  helix:  1.32 (0.17), residues: 984
  sheet: -1.98 (0.76), residues: 54
  loop : -1.82 (0.43), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  19 
 HIS   0.001   0.000   HIS C  41 
 PHE   0.012   0.001   PHE A 218 
 TYR   0.011   0.001   TYR A 373 
 ARG   0.002   0.000   ARG B 445 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A  322 GLN cc_start: 0.7813 (tp40) cc_final: 0.7286 (mm-40)
REVERT: A  342 ARG cc_start: 0.7051 (ppt170) cc_final: 0.6822 (ppt90)
REVERT: A  393 GLN cc_start: 0.8660 (mt0) cc_final: 0.8171 (mt0)
REVERT: A  431 GLU cc_start: 0.7439 (pm20) cc_final: 0.7181 (mp0)
REVERT: A  463 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7436 (tm-30)
REVERT: B   75 MET cc_start: 0.9195 (mmm) cc_final: 0.8855 (tpp)
REVERT: B  200 TYR cc_start: 0.8315 (m-80) cc_final: 0.7966 (m-10)
REVERT: B  248 MET cc_start: 0.9020 (tpp) cc_final: 0.8768 (mmm)
REVERT: B  303 LEU cc_start: 0.8278 (tp) cc_final: 0.7885 (tt)
REVERT: B  322 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7510 (mm-40)
REVERT: B  345 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7023 (mm-30)
REVERT: B  366 ASN cc_start: 0.8174 (t0) cc_final: 0.7908 (t0)
REVERT: B  389 LEU cc_start: 0.7977 (mt) cc_final: 0.7739 (mt)
REVERT: B  431 GLU cc_start: 0.7654 (mp0) cc_final: 0.7446 (mm-30)
REVERT: B  463 GLU cc_start: 0.7843 (tt0) cc_final: 0.7363 (tm-30)
REVERT: B  473 MET cc_start: 0.6719 (ttt) cc_final: 0.6401 (mtp)
REVERT: C  248 MET cc_start: 0.9064 (tpp) cc_final: 0.8762 (mmt)
REVERT: C  280 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6784 (ttm170)
REVERT: C  303 LEU cc_start: 0.8204 (tp) cc_final: 0.7838 (tt)
REVERT: C  322 GLN cc_start: 0.7799 (tp40) cc_final: 0.7310 (mm-40)
REVERT: C  342 ARG cc_start: 0.7344 (ppt170) cc_final: 0.7019 (ppt90)
REVERT: C  351 ASP cc_start: 0.7144 (t0) cc_final: 0.6786 (t0)
REVERT: C  463 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7547 (tm-30)
  outliers start: 28
  outliers final: 12
  residues processed: 169
  average time/residue: 1.1712
  time to fit residues: 212.3986
Evaluate side-chains
  160 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 108 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.101976 restraints weight = 11272.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.75
r_work: 0.2893 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9534  Z= 0.176
  Angle     :  0.502   5.802  12936  Z= 0.256
  Chirality :  0.038   0.129   1644
  Planarity :  0.003   0.036   1572
  Dihedral  :  3.759  18.253   1293
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.26 %
    Favored  : 79.13 %
  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:  1.16 (0.25), residues: 1215
  helix:  1.40 (0.17), residues: 987
  sheet: -1.81 (0.77), residues: 54
  loop : -1.80 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  19 
 HIS   0.001   0.000   HIS C  41 
 PHE   0.017   0.001   PHE C 316 
 TYR   0.013   0.001   TYR C 373 
 ARG   0.002   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 152
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  276 TRP cc_start: 0.7371 (m100) cc_final: 0.7046 (m-90)
REVERT: A  322 GLN cc_start: 0.7820 (tp40) cc_final: 0.7304 (mm-40)
REVERT: A  342 ARG cc_start: 0.7105 (ppt170) cc_final: 0.6867 (ppt90)
REVERT: A  393 GLN cc_start: 0.8660 (mt0) cc_final: 0.8152 (mt0)
REVERT: A  431 GLU cc_start: 0.7414 (pm20) cc_final: 0.7186 (mp0)
REVERT: A  463 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7479 (tm-30)
REVERT: B  200 TYR cc_start: 0.8320 (m-80) cc_final: 0.7949 (m-10)
REVERT: B  248 MET cc_start: 0.9029 (tpp) cc_final: 0.8774 (mmm)
REVERT: B  303 LEU cc_start: 0.8264 (tp) cc_final: 0.7875 (tt)
REVERT: B  322 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7466 (mm-40)
REVERT: B  389 LEU cc_start: 0.7943 (mt) cc_final: 0.7738 (mt)
REVERT: B  463 GLU cc_start: 0.7854 (tt0) cc_final: 0.7405 (tm-30)
REVERT: B  473 MET cc_start: 0.6735 (ttt) cc_final: 0.6415 (mtp)
REVERT: C  248 MET cc_start: 0.9089 (tpp) cc_final: 0.8781 (mmt)
REVERT: C  280 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6834 (ttm170)
REVERT: C  303 LEU cc_start: 0.8231 (tp) cc_final: 0.7850 (tt)
REVERT: C  316 PHE cc_start: 0.7805 (t80) cc_final: 0.7553 (t80)
REVERT: C  322 GLN cc_start: 0.7799 (tp40) cc_final: 0.7329 (mm-40)
REVERT: C  342 ARG cc_start: 0.7349 (ppt170) cc_final: 0.7024 (ppt90)
REVERT: C  351 ASP cc_start: 0.7188 (t0) cc_final: 0.6793 (t0)
REVERT: C  393 GLN cc_start: 0.8664 (mt0) cc_final: 0.8324 (mt0)
REVERT: C  463 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7552 (tm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 166
  average time/residue: 1.1631
  time to fit residues: 207.4153
Evaluate side-chains
  167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B  85 ASN
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.101603 restraints weight = 11174.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.75
r_work: 0.2894 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9534  Z= 0.177
  Angle     :  0.515   7.510  12936  Z= 0.261
  Chirality :  0.038   0.132   1644
  Planarity :  0.003   0.035   1572
  Dihedral  :  3.750  17.839   1293
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.74 %
    Favored  : 78.74 %
  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:  1.45 (0.25), residues: 1215
  helix:  1.62 (0.17), residues: 969
  sheet: -1.85 (0.75), residues: 54
  loop : -1.45 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  19 
 HIS   0.001   0.000   HIS C  41 
 PHE   0.017   0.001   PHE C 316 
 TYR   0.016   0.001   TYR C 373 
 ARG   0.002   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  276 TRP cc_start: 0.7358 (m100) cc_final: 0.7091 (m-90)
REVERT: A  322 GLN cc_start: 0.7744 (tp40) cc_final: 0.7216 (mm-40)
REVERT: A  342 ARG cc_start: 0.7102 (ppt170) cc_final: 0.6854 (ppt90)
REVERT: A  393 GLN cc_start: 0.8661 (mt0) cc_final: 0.8171 (mt0)
REVERT: A  431 GLU cc_start: 0.7337 (pm20) cc_final: 0.7117 (mp0)
REVERT: A  463 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7460 (tm-30)
REVERT: B   75 MET cc_start: 0.9205 (mmm) cc_final: 0.8872 (tpp)
REVERT: B  200 TYR cc_start: 0.8317 (m-80) cc_final: 0.7985 (m-10)
REVERT: B  248 MET cc_start: 0.9036 (tpp) cc_final: 0.8771 (mmm)
REVERT: B  303 LEU cc_start: 0.8258 (tp) cc_final: 0.7857 (tt)
REVERT: B  322 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7418 (mm-40)
REVERT: B  342 ARG cc_start: 0.7346 (ppt170) cc_final: 0.7009 (ppt90)
REVERT: B  366 ASN cc_start: 0.8234 (t0) cc_final: 0.7960 (t0)
REVERT: B  463 GLU cc_start: 0.7887 (tt0) cc_final: 0.7434 (tm-30)
REVERT: B  473 MET cc_start: 0.6642 (ttt) cc_final: 0.6323 (mtp)
REVERT: C  248 MET cc_start: 0.9100 (tpp) cc_final: 0.8784 (mmt)
REVERT: C  280 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6827 (ttm170)
REVERT: C  303 LEU cc_start: 0.8191 (tp) cc_final: 0.7798 (tt)
REVERT: C  316 PHE cc_start: 0.7772 (t80) cc_final: 0.7542 (t80)
REVERT: C  322 GLN cc_start: 0.7777 (tp40) cc_final: 0.7331 (mm-40)
REVERT: C  342 ARG cc_start: 0.7344 (ppt170) cc_final: 0.7005 (ppt90)
REVERT: C  351 ASP cc_start: 0.7260 (t0) cc_final: 0.6849 (t0)
REVERT: C  393 GLN cc_start: 0.8660 (mt0) cc_final: 0.8310 (mt0)
REVERT: C  463 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7535 (tm-30)
  outliers start: 26
  outliers final: 17
  residues processed: 167
  average time/residue: 1.2257
  time to fit residues: 219.4782
Evaluate side-chains
  169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 88 optimal weight:    0.0050
   chunk 96 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 103 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.2398

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B  85 ASN
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.100719 restraints weight = 11267.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.87
r_work: 0.2851 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9534  Z= 0.221
  Angle     :  0.539   7.153  12936  Z= 0.273
  Chirality :  0.039   0.140   1644
  Planarity :  0.003   0.036   1572
  Dihedral  :  3.859  17.754   1293
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.23 %
    Favored  : 78.65 %
  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:  1.20 (0.26), residues: 1215
  helix:  1.45 (0.18), residues: 981
  sheet: -1.80 (0.75), residues: 54
  loop : -1.88 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  19 
 HIS   0.001   0.000   HIS C  41 
 PHE   0.016   0.002   PHE C 316 
 TYR   0.015   0.001   TYR C 373 
 ARG   0.002   0.000   ARG A 353 

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

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

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2430 Ramachandran restraints generated.
    1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  276 TRP cc_start: 0.7331 (m100) cc_final: 0.6937 (m-90)
REVERT: A  279 PHE cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-80)
REVERT: A  322 GLN cc_start: 0.7697 (tp40) cc_final: 0.7162 (mm-40)
REVERT: A  342 ARG cc_start: 0.7067 (ppt170) cc_final: 0.6807 (ppt90)
REVERT: A  393 GLN cc_start: 0.8583 (mt0) cc_final: 0.8041 (mt0)
REVERT: A  431 GLU cc_start: 0.7285 (pm20) cc_final: 0.7031 (mp0)
REVERT: A  463 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: B   75 MET cc_start: 0.9146 (mmm) cc_final: 0.8811 (tpp)
REVERT: B  200 TYR cc_start: 0.8295 (m-80) cc_final: 0.7944 (m-10)
REVERT: B  248 MET cc_start: 0.8992 (tpp) cc_final: 0.8722 (mmm)
REVERT: B  322 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7345 (mm-40)
REVERT: B  342 ARG cc_start: 0.7247 (ppt170) cc_final: 0.6899 (ppt90)
REVERT: B  463 GLU cc_start: 0.7849 (tt0) cc_final: 0.7358 (tm-30)
REVERT: B  473 MET cc_start: 0.6375 (ttt) cc_final: 0.6086 (mtp)
REVERT: C  248 MET cc_start: 0.9088 (tpp) cc_final: 0.8599 (mmt)
REVERT: C  280 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6776 (ttm170)
REVERT: C  322 GLN cc_start: 0.7755 (tp40) cc_final: 0.7305 (mm-40)
REVERT: C  342 ARG cc_start: 0.7287 (ppt170) cc_final: 0.6954 (ppt90)
REVERT: C  351 ASP cc_start: 0.7281 (t0) cc_final: 0.6813 (t0)
REVERT: C  463 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7495 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 162
  average time/residue: 1.2008
  time to fit residues: 208.3891
Evaluate side-chains
  169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  274 GLU
Chi-restraints excluded: chain C residue  280 ARG
Chi-restraints excluded: chain C residue  411 VAL
Chi-restraints excluded: chain C residue  463 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 116 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 104 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
B  85 ASN
C  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.099952 restraints weight = 11207.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 1.87
r_work: 0.2845 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9534  Z= 0.256
  Angle     :  0.556   7.002  12936  Z= 0.282
  Chirality :  0.040   0.146   1644
  Planarity :  0.003   0.037   1572
  Dihedral  :  3.966  17.704   1293
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.32 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1215
  helix:  1.37 (0.17), residues: 978
  sheet: -1.79 (0.74), residues: 54
  loop : -1.99 (0.41), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  19 
 HIS   0.001   0.001   HIS C 296 
 PHE   0.015   0.002   PHE A 218 
 TYR   0.015   0.001   TYR C 373 
 ARG   0.002   0.000   ARG A 445 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7230.02 seconds
wall clock time: 128 minutes 17.15 seconds (7697.15 seconds total)