Starting phenix.real_space_refine
on Thu Sep 18 18:04:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mdr_48178/09_2025/9mdr_48178.map"
  }
  resolution = 3.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.097
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: 5
    Type Number    sf(0)   Gaussians
     Ca     14      9.91       5
     S      35      5.16       5
     C   11529      2.51       5
     N    2989      2.21       5
     O    3822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18389
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2625
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 336, 2616
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 14, 'TRANS': 321}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 336, 2616
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 14, 'TRANS': 321}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2647
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 2.69, per 1000 atoms: 0.15
  Number of scatterers: 18389
  At special positions: 0
  Unit cell: (139.32, 141.04, 96.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca     14     19.99
     S      35     16.00
     O    3822      8.00
     N    2989      7.00
     C   11529      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: 1.25
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4410

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 56 sheets defined
      23.2% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 227 through 234
    Processing helix  chain 'A' and resid 246 through 253
      removed outlier: 3.747A  pdb=" N   ALA A 250 " --> pdb=" O   ASP A 247 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A 253 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 279
    Processing helix  chain 'A' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP A 291 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 473
      removed outlier: 3.748A  pdb=" N   ALA A 472 " --> pdb=" O   LYS A 468 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY A 473 " --> pdb=" O   LYS A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 513
      removed outlier: 3.788A  pdb=" N   SER A 512 " --> pdb=" O   SER A 508 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE A 513 " --> pdb=" O   GLN A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 556
    Processing helix  chain 'A' and resid 581 through 593
      removed outlier: 3.695A  pdb=" N   LYS A 593 " --> pdb=" O   LYS A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN A 602 " --> pdb=" O   LYS A 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 234
    Processing helix  chain 'B' and resid 246 through 253
      removed outlier: 3.748A  pdb=" N   ALA B 250 " --> pdb=" O   ASP B 247 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY B 253 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 279
    Processing helix  chain 'B' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP B 291 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 473
      removed outlier: 3.748A  pdb=" N   ALA B 472 " --> pdb=" O   LYS B 468 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY B 473 " --> pdb=" O   LYS B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 513
      removed outlier: 3.789A  pdb=" N   SER B 512 " --> pdb=" O   SER B 508 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE B 513 " --> pdb=" O   GLN B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 556
    Processing helix  chain 'B' and resid 581 through 593
      removed outlier: 3.695A  pdb=" N   LYS B 593 " --> pdb=" O   LYS B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN B 602 " --> pdb=" O   LYS B 599 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 227 through 234
    Processing helix  chain 'C' and resid 246 through 253
      removed outlier: 3.747A  pdb=" N   ALA C 250 " --> pdb=" O   ASP C 247 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU C 251 " --> pdb=" O   SER C 248 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY C 253 " --> pdb=" O   ALA C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 279
    Processing helix  chain 'C' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP C 291 " --> pdb=" O   GLU C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 473
      removed outlier: 3.747A  pdb=" N   ALA C 472 " --> pdb=" O   LYS C 468 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY C 473 " --> pdb=" O   LYS C 469 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 506 through 513
      removed outlier: 3.789A  pdb=" N   SER C 512 " --> pdb=" O   SER C 508 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE C 513 " --> pdb=" O   GLN C 509 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 546 through 556
    Processing helix  chain 'C' and resid 581 through 593
      removed outlier: 3.696A  pdb=" N   LYS C 593 " --> pdb=" O   LYS C 589 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN C 602 " --> pdb=" O   LYS C 599 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 227 through 234
    Processing helix  chain 'D' and resid 246 through 253
      removed outlier: 3.746A  pdb=" N   ALA D 250 " --> pdb=" O   ASP D 247 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU D 251 " --> pdb=" O   SER D 248 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY D 253 " --> pdb=" O   ALA D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 272 through 279
    Processing helix  chain 'D' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP D 291 " --> pdb=" O   GLU D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 463 through 473
      removed outlier: 3.748A  pdb=" N   ALA D 472 " --> pdb=" O   LYS D 468 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY D 473 " --> pdb=" O   LYS D 469 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 506 through 513
      removed outlier: 3.788A  pdb=" N   SER D 512 " --> pdb=" O   SER D 508 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE D 513 " --> pdb=" O   GLN D 509 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 546 through 556
    Processing helix  chain 'D' and resid 581 through 593
      removed outlier: 3.695A  pdb=" N   LYS D 593 " --> pdb=" O   LYS D 589 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN D 602 " --> pdb=" O   LYS D 599 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 227 through 234
    Processing helix  chain 'E' and resid 246 through 253
      removed outlier: 3.747A  pdb=" N   ALA E 250 " --> pdb=" O   ASP E 247 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU E 251 " --> pdb=" O   SER E 248 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY E 253 " --> pdb=" O   ALA E 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 272 through 279
    Processing helix  chain 'E' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP E 291 " --> pdb=" O   GLU E 288 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 463 through 473
      removed outlier: 3.747A  pdb=" N   ALA E 472 " --> pdb=" O   LYS E 468 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY E 473 " --> pdb=" O   LYS E 469 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 506 through 513
      removed outlier: 3.788A  pdb=" N   SER E 512 " --> pdb=" O   SER E 508 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE E 513 " --> pdb=" O   GLN E 509 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 546 through 556
    Processing helix  chain 'E' and resid 581 through 593
      removed outlier: 3.695A  pdb=" N   LYS E 593 " --> pdb=" O   LYS E 589 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN E 602 " --> pdb=" O   LYS E 599 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 227 through 234
    Processing helix  chain 'F' and resid 246 through 253
      removed outlier: 3.747A  pdb=" N   ALA F 250 " --> pdb=" O   ASP F 247 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU F 251 " --> pdb=" O   SER F 248 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY F 253 " --> pdb=" O   ALA F 250 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 272 through 279
    Processing helix  chain 'F' and resid 286 through 291
      removed outlier: 3.879A  pdb=" N   ASP F 291 " --> pdb=" O   GLU F 288 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 463 through 473
      removed outlier: 3.747A  pdb=" N   ALA F 472 " --> pdb=" O   LYS F 468 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY F 473 " --> pdb=" O   LYS F 469 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 506 through 513
      removed outlier: 3.788A  pdb=" N   SER F 512 " --> pdb=" O   SER F 508 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE F 513 " --> pdb=" O   GLN F 509 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 546 through 556
    Processing helix  chain 'F' and resid 581 through 593
      removed outlier: 3.696A  pdb=" N   LYS F 593 " --> pdb=" O   LYS F 589 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN F 602 " --> pdb=" O   LYS F 599 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 227 through 234
    Processing helix  chain 'G' and resid 246 through 253
      removed outlier: 3.747A  pdb=" N   ALA G 250 " --> pdb=" O   ASP G 247 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU G 251 " --> pdb=" O   SER G 248 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY G 253 " --> pdb=" O   ALA G 250 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 272 through 279
    Processing helix  chain 'G' and resid 286 through 291
      removed outlier: 3.878A  pdb=" N   ASP G 291 " --> pdb=" O   GLU G 288 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 463 through 473
      removed outlier: 3.748A  pdb=" N   ALA G 472 " --> pdb=" O   LYS G 468 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY G 473 " --> pdb=" O   LYS G 469 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 506 through 513
      removed outlier: 3.788A  pdb=" N   SER G 512 " --> pdb=" O   SER G 508 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE G 513 " --> pdb=" O   GLN G 509 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 546 through 556
    Processing helix  chain 'G' and resid 581 through 593
      removed outlier: 3.695A  pdb=" N   LYS G 593 " --> pdb=" O   LYS G 589 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 599 through 603
      removed outlier: 3.553A  pdb=" N   ASN G 602 " --> pdb=" O   LYS G 599 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311
      removed outlier: 4.271A  pdb=" N   LEU A 307 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN A 390 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE A 309 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   TYR A 388 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 311
      removed outlier: 4.271A  pdb=" N   LEU A 307 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN A 390 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE A 309 " --> pdb=" O   TYR A 388 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   TYR A 388 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 387 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS A 405 " --> pdb=" O   ASN A 431 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASN A 431 " --> pdb=" O   LYS A 405 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423
      removed outlier: 3.882A  pdb=" N   SER A 420 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR A 409 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490
    Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531
    Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 238
    Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 311
      removed outlier: 4.271A  pdb=" N   LEU B 307 " --> pdb=" O   ASN B 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN B 390 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE B 309 " --> pdb=" O   TYR B 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR B 388 " --> pdb=" O   ILE B 309 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 298 through 311
      removed outlier: 4.271A  pdb=" N   LEU B 307 " --> pdb=" O   ASN B 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN B 390 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE B 309 " --> pdb=" O   TYR B 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR B 388 " --> pdb=" O   ILE B 309 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B 387 " --> pdb=" O   ILE B 462 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS B 405 " --> pdb=" O   ASN B 431 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASN B 431 " --> pdb=" O   LYS B 405 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 423
      removed outlier: 3.883A  pdb=" N   SER B 420 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR B 409 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490
    Processing sheet with id=AB6, first strand: chain 'B' and resid 525 through 531
    Processing sheet with id=AB7, first strand: chain 'B' and resid 559 through 560
    Processing sheet with id=AB8, first strand: chain 'C' and resid 235 through 238
    Processing sheet with id=AB9, first strand: chain 'C' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU C 307 " --> pdb=" O   ASN C 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN C 390 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE C 309 " --> pdb=" O   TYR C 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR C 388 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU C 307 " --> pdb=" O   ASN C 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN C 390 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE C 309 " --> pdb=" O   TYR C 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR C 388 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA C 387 " --> pdb=" O   ILE C 462 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 403 through 406
      removed outlier: 6.085A  pdb=" N   LYS C 405 " --> pdb=" O   ASN C 431 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ASN C 431 " --> pdb=" O   LYS C 405 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 418 through 423
      removed outlier: 3.883A  pdb=" N   SER C 420 " --> pdb=" O   LEU C 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR C 409 " --> pdb=" O   THR C 481 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 490
    Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 531
    Processing sheet with id=AC6, first strand: chain 'C' and resid 559 through 560
    Processing sheet with id=AC7, first strand: chain 'D' and resid 235 through 238
    Processing sheet with id=AC8, first strand: chain 'D' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU D 307 " --> pdb=" O   ASN D 390 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN D 390 " --> pdb=" O   LEU D 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE D 309 " --> pdb=" O   TYR D 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR D 388 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'D' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU D 307 " --> pdb=" O   ASN D 390 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN D 390 " --> pdb=" O   LEU D 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE D 309 " --> pdb=" O   TYR D 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR D 388 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA D 387 " --> pdb=" O   ILE D 462 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS D 405 " --> pdb=" O   ASN D 431 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASN D 431 " --> pdb=" O   LYS D 405 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'D' and resid 418 through 423
      removed outlier: 3.883A  pdb=" N   SER D 420 " --> pdb=" O   LEU D 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR D 409 " --> pdb=" O   THR D 481 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 489 through 490
    Processing sheet with id=AD4, first strand: chain 'D' and resid 525 through 531
    Processing sheet with id=AD5, first strand: chain 'D' and resid 559 through 560
    Processing sheet with id=AD6, first strand: chain 'E' and resid 235 through 238
    Processing sheet with id=AD7, first strand: chain 'E' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU E 307 " --> pdb=" O   ASN E 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN E 390 " --> pdb=" O   LEU E 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE E 309 " --> pdb=" O   TYR E 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR E 388 " --> pdb=" O   ILE E 309 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'E' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU E 307 " --> pdb=" O   ASN E 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN E 390 " --> pdb=" O   LEU E 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE E 309 " --> pdb=" O   TYR E 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR E 388 " --> pdb=" O   ILE E 309 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA E 387 " --> pdb=" O   ILE E 462 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'E' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS E 405 " --> pdb=" O   ASN E 431 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ASN E 431 " --> pdb=" O   LYS E 405 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'E' and resid 418 through 423
      removed outlier: 3.883A  pdb=" N   SER E 420 " --> pdb=" O   LEU E 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR E 409 " --> pdb=" O   THR E 481 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'E' and resid 489 through 490
    Processing sheet with id=AE3, first strand: chain 'E' and resid 525 through 531
    Processing sheet with id=AE4, first strand: chain 'E' and resid 559 through 560
    Processing sheet with id=AE5, first strand: chain 'F' and resid 235 through 238
    Processing sheet with id=AE6, first strand: chain 'F' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU F 307 " --> pdb=" O   ASN F 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN F 390 " --> pdb=" O   LEU F 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE F 309 " --> pdb=" O   TYR F 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR F 388 " --> pdb=" O   ILE F 309 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'F' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU F 307 " --> pdb=" O   ASN F 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN F 390 " --> pdb=" O   LEU F 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE F 309 " --> pdb=" O   TYR F 388 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR F 388 " --> pdb=" O   ILE F 309 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA F 387 " --> pdb=" O   ILE F 462 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'F' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS F 405 " --> pdb=" O   ASN F 431 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ASN F 431 " --> pdb=" O   LYS F 405 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'F' and resid 418 through 423
      removed outlier: 3.882A  pdb=" N   SER F 420 " --> pdb=" O   LEU F 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR F 409 " --> pdb=" O   THR F 481 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'F' and resid 489 through 490
    Processing sheet with id=AF2, first strand: chain 'F' and resid 525 through 531
    Processing sheet with id=AF3, first strand: chain 'F' and resid 559 through 560
    Processing sheet with id=AF4, first strand: chain 'G' and resid 235 through 238
    Processing sheet with id=AF5, first strand: chain 'G' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU G 307 " --> pdb=" O   ASN G 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN G 390 " --> pdb=" O   LEU G 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE G 309 " --> pdb=" O   TYR G 388 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR G 388 " --> pdb=" O   ILE G 309 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'G' and resid 298 through 311
      removed outlier: 4.270A  pdb=" N   LEU G 307 " --> pdb=" O   ASN G 390 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   ASN G 390 " --> pdb=" O   LEU G 307 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ILE G 309 " --> pdb=" O   TYR G 388 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR G 388 " --> pdb=" O   ILE G 309 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA G 387 " --> pdb=" O   ILE G 462 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'G' and resid 403 through 406
      removed outlier: 6.084A  pdb=" N   LYS G 405 " --> pdb=" O   ASN G 431 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ASN G 431 " --> pdb=" O   LYS G 405 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'G' and resid 418 through 423
      removed outlier: 3.883A  pdb=" N   SER G 420 " --> pdb=" O   LEU G 412 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   THR G 409 " --> pdb=" O   THR G 481 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'G' and resid 489 through 490
    Processing sheet with id=AG1, first strand: chain 'G' and resid 525 through 531
    Processing sheet with id=AG2, first strand: chain 'G' and resid 559 through 560

    616 hydrogen bonds defined for protein.
    1582 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: 2.18

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6041
        1.34 -     1.46: 3258
        1.46 -     1.57: 9321
        1.57 -     1.69: 0
        1.69 -     1.81: 63
  Bond restraints: 18683
  Sorted by residual:
  bond pdb=" C   TYR B 439 "
       pdb=" N   PRO B 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.67e+00
  bond pdb=" C   TYR D 439 "
       pdb=" N   PRO D 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.66e+00
  bond pdb=" C   TYR E 439 "
       pdb=" N   PRO E 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.60e+00
  bond pdb=" C   TYR F 439 "
       pdb=" N   PRO F 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.59e+00
  bond pdb=" C   TYR A 439 "
       pdb=" N   PRO A 440 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.58e+00
  ... (remaining 18678 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 24524
        1.51 -     3.01: 606
        3.01 -     4.52: 126
        4.52 -     6.02: 35
        6.02 -     7.53: 35
  Bond angle restraints: 25326
  Sorted by residual:
  angle pdb=" C   ASN D 431 "
        pdb=" N   ASN D 432 "
        pdb=" CA  ASN D 432 "
      ideal   model   delta    sigma   weight residual
     122.82  128.72   -5.90 1.42e+00 4.96e-01 1.73e+01
  angle pdb=" C   ASN C 431 "
        pdb=" N   ASN C 432 "
        pdb=" CA  ASN C 432 "
      ideal   model   delta    sigma   weight residual
     122.82  128.71   -5.89 1.42e+00 4.96e-01 1.72e+01
  angle pdb=" C   ASN E 431 "
        pdb=" N   ASN E 432 "
        pdb=" CA  ASN E 432 "
      ideal   model   delta    sigma   weight residual
     122.82  128.71   -5.89 1.42e+00 4.96e-01 1.72e+01
  angle pdb=" C   ASN F 431 "
        pdb=" N   ASN F 432 "
        pdb=" CA  ASN F 432 "
      ideal   model   delta    sigma   weight residual
     122.82  128.69   -5.87 1.42e+00 4.96e-01 1.71e+01
  angle pdb=" C   ASN B 431 "
        pdb=" N   ASN B 432 "
        pdb=" CA  ASN B 432 "
      ideal   model   delta    sigma   weight residual
     122.82  128.69   -5.87 1.42e+00 4.96e-01 1.71e+01
  ... (remaining 25321 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 9558
       17.27 -    34.54: 1327
       34.54 -    51.81: 462
       51.81 -    69.08: 70
       69.08 -    86.34: 28
  Dihedral angle restraints: 11445
    sinusoidal: 4550
      harmonic: 6895
  Sorted by residual:
  dihedral pdb=" CA  TYR A 439 "
           pdb=" C   TYR A 439 "
           pdb=" N   PRO A 440 "
           pdb=" CA  PRO A 440 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TYR E 439 "
           pdb=" C   TYR E 439 "
           pdb=" N   PRO E 440 "
           pdb=" CA  PRO E 440 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.67   16.33     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" CA  TYR D 439 "
           pdb=" C   TYR D 439 "
           pdb=" N   PRO D 440 "
           pdb=" CA  PRO D 440 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.69   16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 11442 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1929
       0.039 -    0.079: 668
       0.079 -    0.118: 218
       0.118 -    0.157: 41
       0.157 -    0.197: 21
  Chirality restraints: 2877
  Sorted by residual:
  chirality pdb=" CB  ILE A 569 "
            pdb=" CA  ILE A 569 "
            pdb=" CG1 ILE A 569 "
            pdb=" CG2 ILE A 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CB  ILE E 569 "
            pdb=" CA  ILE E 569 "
            pdb=" CG1 ILE E 569 "
            pdb=" CG2 ILE E 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CB  ILE B 569 "
            pdb=" CA  ILE B 569 "
            pdb=" CG1 ILE B 569 "
            pdb=" CG2 ILE B 569 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.47e-01
  ... (remaining 2874 not shown)

  Planarity restraints: 3297
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 269 "   -0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO E 270 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO E 270 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 270 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G 269 "    0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO G 270 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO G 270 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO G 270 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 269 "   -0.024 5.00e-02 4.00e+02   3.69e-02 2.18e+00
        pdb=" N   PRO D 270 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO D 270 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO D 270 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 3294 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 6158
        2.84 -     3.35: 14674
        3.35 -     3.87: 28938
        3.87 -     4.38: 32386
        4.38 -     4.90: 60103
  Nonbonded interactions: 142259
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 540 "
            pdb=" OG1 THR C 542 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD1 ASP E 540 "
            pdb=" OG1 THR E 542 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD1 ASP B 540 "
            pdb=" OG1 THR B 542 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD1 ASP D 540 "
            pdb=" OG1 THR D 542 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OD1 ASP G 540 "
            pdb=" OG1 THR G 542 "
     model   vdw
     2.322 3.040
  ... (remaining 142254 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 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.320
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
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      :  0.003   0.030  18683  Z= 0.129
  Angle     :  0.641   7.531  25326  Z= 0.346
  Chirality :  0.046   0.197   2877
  Planarity :  0.004   0.037   3297
  Dihedral  : 18.003  86.344   7035
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 29.25 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.16), residues: 2331
  helix: -1.62 (0.22), residues: 406
  sheet:  0.59 (0.22), residues: 581
  loop : -1.68 (0.15), residues: 1344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 394 
 TYR   0.008   0.001   TYR B 230 
 PHE   0.009   0.001   PHE F 487 
 TRP   0.005   0.001   TRP E 503 
 HIS   0.001   0.001   HIS G 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (18683)
  covalent geometry    : angle       0.64079 (25326)
  hydrogen bonds       : bond        0.16600 (  560)
  hydrogen bonds       : angle       7.57666 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 204
  time to evaluate  : 0.743 
Fit side-chains
REVERT: B  252 GLN cc_start: 0.8124 (mt0) cc_final: 0.7908 (mt0)
REVERT: D  565 TYR cc_start: 0.7866 (m-80) cc_final: 0.7225 (m-80)
REVERT: E  565 TYR cc_start: 0.7698 (m-80) cc_final: 0.7021 (m-80)
  outliers start: 8
  outliers final: 7
  residues processed: 205
  average time/residue: 0.1118
  time to fit residues: 37.3736
Evaluate side-chains
  206 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 199
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain C residue  590 ASP
Chi-restraints excluded: chain D residue  379 LEU
Chi-restraints excluded: chain D residue  590 ASP
Chi-restraints excluded: chain G residue  379 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 216 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 194 optimal weight:    5.9990
   chunk 227 optimal weight:    4.9990
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 200 optimal weight:    0.0030
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
A 501 ASN
B 454 GLN
B 501 ASN
C 475 GLN
C 501 ASN
D 454 GLN
D 501 ASN
E 501 ASN
F 501 ASN
G 501 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.140023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.112534 restraints weight = 38865.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 3.10
r_work: 0.3213 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.0722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  18683  Z= 0.120
  Angle     :  0.525   5.954  25326  Z= 0.280
  Chirality :  0.042   0.157   2877
  Planarity :  0.004   0.033   3297
  Dihedral  :  4.309  32.051   2548
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.36 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.17), residues: 2331
  helix: -0.77 (0.25), residues: 420
  sheet:  0.72 (0.22), residues: 574
  loop : -1.60 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 394 
 TYR   0.008   0.001   TYR F 230 
 PHE   0.009   0.001   PHE C 487 
 TRP   0.005   0.001   TRP G 503 
 HIS   0.000   0.000   HIS F 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (18683)
  covalent geometry    : angle       0.52465 (25326)
  hydrogen bonds       : bond        0.03101 (  560)
  hydrogen bonds       : angle       5.65851 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 213
  time to evaluate  : 0.504 
Fit side-chains
REVERT: C  586 ASN cc_start: 0.8564 (m-40) cc_final: 0.8075 (m110)
REVERT: E  505 ASP cc_start: 0.8336 (p0) cc_final: 0.8048 (p0)
REVERT: E  565 TYR cc_start: 0.8024 (m-80) cc_final: 0.7561 (m-80)
  outliers start: 57
  outliers final: 32
  residues processed: 262
  average time/residue: 0.1044
  time to fit residues: 45.3224
Evaluate side-chains
  227 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  478 LEU
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  478 LEU
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  379 LEU
Chi-restraints excluded: chain F residue  478 LEU
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  311 THR
Chi-restraints excluded: chain G residue  478 LEU
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0970
   chunk 108 optimal weight:    9.9990
   chunk 228 optimal weight:    7.9990
   chunk 170 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 208 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0470
   overall best weight:    1.1680

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

Flipped N/Q/H residues before XYZ refinement:
B 314 HIS
B 454 GLN
D 454 GLN
F 454 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.138511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.110778 restraints weight = 63662.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 4.04
r_work: 0.3145 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  18683  Z= 0.127
  Angle     :  0.530   6.179  25326  Z= 0.283
  Chirality :  0.043   0.157   2877
  Planarity :  0.003   0.029   3297
  Dihedral  :  4.049  14.076   2534
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 27.60 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.17), residues: 2331
  helix: -0.50 (0.26), residues: 420
  sheet:  0.68 (0.22), residues: 574
  loop : -1.58 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 394 
 TYR   0.010   0.001   TYR E 395 
 PHE   0.009   0.001   PHE E 555 
 TRP   0.005   0.001   TRP F 503 
 HIS   0.001   0.000   HIS F 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (18683)
  covalent geometry    : angle       0.53025 (25326)
  hydrogen bonds       : bond        0.02953 (  560)
  hydrogen bonds       : angle       5.43859 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 204
  time to evaluate  : 0.717 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.8079 (m-80) cc_final: 0.7618 (m-80)
  outliers start: 53
  outliers final: 42
  residues processed: 242
  average time/residue: 0.1096
  time to fit residues: 43.1599
Evaluate side-chains
  232 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 190
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  502 SER
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  478 LEU
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain D residue  502 SER
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  478 LEU
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  478 LEU
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  311 THR
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  478 LEU
Chi-restraints excluded: chain G residue  496 ILE
Chi-restraints excluded: chain G residue  502 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 154 optimal weight:    2.9990
   chunk 195 optimal weight:    0.5980
   chunk 102 optimal weight:    0.8980
   chunk 143 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 230 optimal weight:    7.9990
   chunk 186 optimal weight:   10.0000
   chunk 141 optimal weight:    9.9990
   chunk 209 optimal weight:    4.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
A 314 HIS
A 454 GLN
B 454 GLN
C 314 HIS
D 314 HIS
E 314 HIS
F 314 HIS
F 454 GLN
G 314 HIS
G 432 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.110526 restraints weight = 58858.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.91
r_work: 0.3116 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18683  Z= 0.131
  Angle     :  0.529   6.235  25326  Z= 0.283
  Chirality :  0.043   0.165   2877
  Planarity :  0.003   0.030   3297
  Dihedral  :  4.033  14.053   2534
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 27.55 %
    Favored  : 69.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.17), residues: 2331
  helix: -0.40 (0.26), residues: 420
  sheet:  0.69 (0.22), residues: 574
  loop : -1.59 (0.15), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 394 
 TYR   0.009   0.001   TYR A 395 
 PHE   0.009   0.001   PHE B 555 
 TRP   0.005   0.001   TRP A 503 
 HIS   0.001   0.000   HIS F 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (18683)
  covalent geometry    : angle       0.52894 (25326)
  hydrogen bonds       : bond        0.02907 (  560)
  hydrogen bonds       : angle       5.35578 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 204
  time to evaluate  : 0.694 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.8119 (m-80) cc_final: 0.7698 (m-80)
  outliers start: 61
  outliers final: 52
  residues processed: 245
  average time/residue: 0.1102
  time to fit residues: 44.2005
Evaluate side-chains
  248 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 196
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  468 LYS
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  502 SER
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  403 MET
Chi-restraints excluded: chain D residue  468 LYS
Chi-restraints excluded: chain D residue  478 LEU
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain D residue  502 SER
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  478 LEU
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  403 MET
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  478 LEU
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  311 THR
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  478 LEU
Chi-restraints excluded: chain G residue  496 ILE
Chi-restraints excluded: chain G residue  502 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 198 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 206 optimal weight:    0.8980
   chunk 166 optimal weight:    0.8980
   chunk 184 optimal weight:    0.9980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
F 454 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.138748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.111708 restraints weight = 39836.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.08
r_work: 0.3211 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  18683  Z= 0.097
  Angle     :  0.490   5.925  25326  Z= 0.262
  Chirality :  0.042   0.180   2877
  Planarity :  0.003   0.031   3297
  Dihedral  :  3.847  13.566   2534
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 28.33 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.17), residues: 2331
  helix: -0.24 (0.27), residues: 420
  sheet:  0.75 (0.22), residues: 574
  loop : -1.53 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 394 
 TYR   0.007   0.001   TYR A 230 
 PHE   0.006   0.001   PHE G 487 
 TRP   0.005   0.001   TRP A 503 
 HIS   0.000   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (18683)
  covalent geometry    : angle       0.48997 (25326)
  hydrogen bonds       : bond        0.02509 (  560)
  hydrogen bonds       : angle       5.10786 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 214
  time to evaluate  : 0.692 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.8011 (m-80) cc_final: 0.7616 (m-80)
  outliers start: 52
  outliers final: 46
  residues processed: 249
  average time/residue: 0.1000
  time to fit residues: 40.7442
Evaluate side-chains
  248 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 202
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  468 LYS
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  468 LYS
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain D residue  502 SER
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 174 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 194 optimal weight:    4.9990
   chunk 124 optimal weight:    5.9990
   chunk 60 optimal weight:    0.6980
   chunk 178 optimal weight:    1.9990
   chunk 138 optimal weight:    0.9980
   chunk 216 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
F 454 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.136001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.108505 restraints weight = 49900.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 3.39
r_work: 0.3090 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18683  Z= 0.138
  Angle     :  0.535   6.171  25326  Z= 0.285
  Chirality :  0.043   0.198   2877
  Planarity :  0.003   0.029   3297
  Dihedral  :  4.001  13.525   2534
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.47 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.17), residues: 2331
  helix: -0.32 (0.26), residues: 420
  sheet:  0.67 (0.22), residues: 574
  loop : -1.53 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 394 
 TYR   0.010   0.001   TYR B 395 
 PHE   0.011   0.001   PHE E 555 
 TRP   0.006   0.001   TRP G 503 
 HIS   0.000   0.000   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (18683)
  covalent geometry    : angle       0.53490 (25326)
  hydrogen bonds       : bond        0.02900 (  560)
  hydrogen bonds       : angle       5.21208 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 203
  time to evaluate  : 0.429 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.8043 (m-80) cc_final: 0.7633 (m-80)
REVERT: G  606 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7878 (mm-30)
  outliers start: 59
  outliers final: 51
  residues processed: 243
  average time/residue: 0.1024
  time to fit residues: 40.8498
Evaluate side-chains
  239 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 188
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  468 LYS
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  403 MET
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  468 LYS
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain D residue  502 SER
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  403 MET
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  468 LYS
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 224 optimal weight:    0.9990
   chunk 221 optimal weight:    7.9990
   chunk 206 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 167 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 216 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 181 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
E 454 GLN
F 454 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108760 restraints weight = 45810.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 3.42
r_work: 0.3124 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  18683  Z= 0.107
  Angle     :  0.506   6.683  25326  Z= 0.269
  Chirality :  0.042   0.183   2877
  Planarity :  0.003   0.031   3297
  Dihedral  :  3.887  13.299   2534
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 28.77 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.17), residues: 2331
  helix: -0.22 (0.26), residues: 420
  sheet:  0.67 (0.22), residues: 574
  loop : -1.50 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 394 
 TYR   0.007   0.001   TYR A 230 
 PHE   0.007   0.001   PHE E 555 
 TRP   0.005   0.001   TRP E 503 
 HIS   0.000   0.000   HIS C 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (18683)
  covalent geometry    : angle       0.50556 (25326)
  hydrogen bonds       : bond        0.02606 (  560)
  hydrogen bonds       : angle       5.07700 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 209
  time to evaluate  : 0.557 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.7888 (m-80) cc_final: 0.7463 (m-80)
  outliers start: 61
  outliers final: 49
  residues processed: 249
  average time/residue: 0.1045
  time to fit residues: 42.7223
Evaluate side-chains
  243 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 194
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  502 SER
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  403 MET
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  468 LYS
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain D residue  502 SER
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  468 LYS
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 37 optimal weight:    0.4980
   chunk 196 optimal weight:    5.9990
   chunk 120 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 169 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0070
   chunk 168 optimal weight:    1.9990
   chunk 160 optimal weight:    0.9980
   chunk 205 optimal weight:    0.6980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
E 454 GLN
F 454 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.139716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.113009 restraints weight = 47175.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 3.19
r_work: 0.3179 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  18683  Z= 0.089
  Angle     :  0.478   6.901  25326  Z= 0.254
  Chirality :  0.042   0.175   2877
  Planarity :  0.003   0.031   3297
  Dihedral  :  3.690  12.990   2534
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 29.40 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.17), residues: 2331
  helix: -0.08 (0.27), residues: 420
  sheet:  0.74 (0.22), residues: 574
  loop : -1.46 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 394 
 TYR   0.006   0.001   TYR F 230 
 PHE   0.005   0.001   PHE E 555 
 TRP   0.005   0.001   TRP G 503 
 HIS   0.001   0.000   HIS C 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 (18683)
  covalent geometry    : angle       0.47804 (25326)
  hydrogen bonds       : bond        0.02289 (  560)
  hydrogen bonds       : angle       4.84926 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 206
  time to evaluate  : 0.727 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.8030 (m-80) cc_final: 0.7635 (m-80)
  outliers start: 49
  outliers final: 44
  residues processed: 241
  average time/residue: 0.1002
  time to fit residues: 39.6602
Evaluate side-chains
  242 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 198
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  307 LEU
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  311 THR
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 123 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 134 optimal weight:    0.0980
   chunk 173 optimal weight:    0.8980
   chunk 164 optimal weight:    7.9990
   chunk 75 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 220 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN
B 454 GLN
C 432 ASN
E 454 GLN
F 454 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.139408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110880 restraints weight = 52155.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 3.71
r_work: 0.3113 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  18683  Z= 0.097
  Angle     :  0.493   6.898  25326  Z= 0.261
  Chirality :  0.042   0.176   2877
  Planarity :  0.003   0.030   3297
  Dihedral  :  3.695  13.032   2534
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 29.30 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.17), residues: 2331
  helix: -0.05 (0.27), residues: 420
  sheet:  0.74 (0.22), residues: 574
  loop : -1.43 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 394 
 TYR   0.006   0.001   TYR A 230 
 PHE   0.006   0.001   PHE E 555 
 TRP   0.006   0.001   TRP B 503 
 HIS   0.001   0.000   HIS B 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (18683)
  covalent geometry    : angle       0.49263 (25326)
  hydrogen bonds       : bond        0.02380 (  560)
  hydrogen bonds       : angle       4.83613 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 202
  time to evaluate  : 0.735 
Fit side-chains
REVERT: C  432 ASN cc_start: 0.9379 (OUTLIER) cc_final: 0.9123 (p0)
REVERT: E  565 TYR cc_start: 0.7932 (m-80) cc_final: 0.7510 (m-80)
  outliers start: 49
  outliers final: 46
  residues processed: 236
  average time/residue: 0.1103
  time to fit residues: 42.5831
Evaluate side-chains
  243 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  432 ASN
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  403 MET
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  468 LYS
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 216 optimal weight:    4.9990
   chunk 145 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 188 optimal weight:    0.3980
   chunk 201 optimal weight:    4.9990
   chunk 226 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
E 454 GLN
F 454 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111147 restraints weight = 36716.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.99
r_work: 0.3171 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  18683  Z= 0.142
  Angle     :  0.681  59.200  25326  Z= 0.393
  Chirality :  0.044   0.515   2877
  Planarity :  0.003   0.062   3297
  Dihedral  :  3.704  13.150   2534
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 29.30 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.17), residues: 2331
  helix: -0.06 (0.27), residues: 420
  sheet:  0.75 (0.22), residues: 574
  loop : -1.43 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 394 
 TYR   0.006   0.001   TYR A 230 
 PHE   0.007   0.001   PHE E 555 
 TRP   0.006   0.001   TRP B 503 
 HIS   0.001   0.000   HIS B 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (18683)
  covalent geometry    : angle       0.68148 (25326)
  hydrogen bonds       : bond        0.02467 (  560)
  hydrogen bonds       : angle       4.83492 ( 1582)

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

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

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4662 Ramachandran restraints generated.
    2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 197
  time to evaluate  : 0.713 
Fit side-chains
REVERT: E  565 TYR cc_start: 0.7948 (m-80) cc_final: 0.7539 (m-80)
  outliers start: 52
  outliers final: 47
  residues processed: 233
  average time/residue: 0.1043
  time to fit residues: 39.9179
Evaluate side-chains
  243 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 196
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  265 ASN
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain B residue  265 ASN
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  403 MET
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain C residue  225 ASN
Chi-restraints excluded: chain C residue  265 ASN
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  406 VAL
Chi-restraints excluded: chain C residue  431 ASN
Chi-restraints excluded: chain C residue  496 ILE
Chi-restraints excluded: chain C residue  605 LEU
Chi-restraints excluded: chain D residue  225 ASN
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  403 MET
Chi-restraints excluded: chain D residue  431 ASN
Chi-restraints excluded: chain D residue  496 ILE
Chi-restraints excluded: chain E residue  225 ASN
Chi-restraints excluded: chain E residue  265 ASN
Chi-restraints excluded: chain E residue  308 ILE
Chi-restraints excluded: chain E residue  311 THR
Chi-restraints excluded: chain E residue  403 MET
Chi-restraints excluded: chain E residue  431 ASN
Chi-restraints excluded: chain E residue  496 ILE
Chi-restraints excluded: chain E residue  502 SER
Chi-restraints excluded: chain F residue  265 ASN
Chi-restraints excluded: chain F residue  308 ILE
Chi-restraints excluded: chain F residue  311 THR
Chi-restraints excluded: chain F residue  431 ASN
Chi-restraints excluded: chain F residue  496 ILE
Chi-restraints excluded: chain G residue  225 ASN
Chi-restraints excluded: chain G residue  265 ASN
Chi-restraints excluded: chain G residue  308 ILE
Chi-restraints excluded: chain G residue  403 MET
Chi-restraints excluded: chain G residue  431 ASN
Chi-restraints excluded: chain G residue  468 LYS
Chi-restraints excluded: chain G residue  496 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 231
   random chunks:
   chunk 174 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 221 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 120 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 454 GLN
** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 454 GLN
F 454 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.139093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110615 restraints weight = 39256.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 3.15
r_work: 0.3159 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  18683  Z= 0.142
  Angle     :  0.681  59.200  25326  Z= 0.393
  Chirality :  0.044   0.515   2877
  Planarity :  0.003   0.062   3297
  Dihedral  :  3.704  13.150   2534
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 29.54 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.17), residues: 2331
  helix: -0.06 (0.27), residues: 420
  sheet:  0.75 (0.22), residues: 574
  loop : -1.43 (0.16), residues: 1337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 394 
 TYR   0.006   0.001   TYR A 230 
 PHE   0.007   0.001   PHE E 555 
 TRP   0.006   0.001   TRP B 503 
 HIS   0.001   0.000   HIS B 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (18683)
  covalent geometry    : angle       0.68148 (25326)
  hydrogen bonds       : bond        0.02467 (  560)
  hydrogen bonds       : angle       4.83492 ( 1582)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3614.06 seconds
wall clock time: 62 minutes 46.98 seconds (3766.98 seconds total)