Starting phenix.real_space_refine
on Sat Aug 23 23:44:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6aye_7018/08_2025/6aye_7018.map"
  }
  resolution = 4.06
  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=   0.002 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     128      5.16       5
     C   10288      2.51       5
     N    2488      2.21       5
     O    2760      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15664
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3916
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 9, 'TRANS': 466}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3916
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 9, 'TRANS': 466}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 3916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3916
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 9, 'TRANS': 466}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 3916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 476, 3916
          Classifications: {'peptide': 476}
          Link IDs: {'PTRANS': 9, 'TRANS': 466}
          Chain breaks: 3
  Time building chain proxies: 3.02, per 1000 atoms: 0.19
  Number of scatterers: 15664
  At special positions: 0
  Unit cell: (106.92, 106.92, 117.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     128     16.00
     O    2760      8.00
     N    2488      7.00
     C   10288      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: 1.08
  Conformation dependent library (CDL) restraints added in 635.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      66.2% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 47
    Processing helix  chain 'A' and resid 49 through 56
      removed outlier: 3.771A  pdb=" N   PHE A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 103
      removed outlier: 3.823A  pdb=" N   ALA A  64 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN A  66 " --> pdb=" O   LYS A  62 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLU A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 135
    Processing helix  chain 'A' and resid 135 through 140
    Processing helix  chain 'A' and resid 226 through 233
      removed outlier: 3.935A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   HIS A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 324
      removed outlier: 4.147A  pdb=" N   PHE A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA A 290 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
      removed outlier: 3.603A  pdb=" N   VAL A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 366
      removed outlier: 3.894A  pdb=" N   MET A 344 " --> pdb=" O   GLY A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 395
      removed outlier: 4.305A  pdb=" N   ILE A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE A 394 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE A 395 " --> pdb=" O   TYR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 435
      removed outlier: 4.336A  pdb=" N   LEU A 401 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
      removed outlier: 3.934A  pdb=" N   ARG A 414 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 422 " --> pdb=" O   CYS A 418 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE A 428 " --> pdb=" O   LEU A 424 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 456
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.717A  pdb=" N   THR A 463 " --> pdb=" O   ASP A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 492
    Processing helix  chain 'A' and resid 492 through 514
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'B' and resid 34 through 47
    Processing helix  chain 'B' and resid 49 through 56
      removed outlier: 3.771A  pdb=" N   PHE B  53 " --> pdb=" O   PRO B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 103
      removed outlier: 3.822A  pdb=" N   ALA B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLN B  66 " --> pdb=" O   LYS B  62 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLU B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 135
    Processing helix  chain 'B' and resid 135 through 140
    Processing helix  chain 'B' and resid 226 through 233
      removed outlier: 3.936A  pdb=" N   VAL B 230 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   HIS B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 324
      removed outlier: 4.150A  pdb=" N   PHE B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ALA B 290 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 338
      removed outlier: 3.603A  pdb=" N   VAL B 338 " --> pdb=" O   GLN B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 366
      removed outlier: 3.895A  pdb=" N   MET B 344 " --> pdb=" O   GLY B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 395
      removed outlier: 4.305A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 385 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG B 390 " --> pdb=" O   LEU B 386 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE B 395 " --> pdb=" O   TYR B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 435
      removed outlier: 4.335A  pdb=" N   LEU B 401 " --> pdb=" O   LYS B 397 " (cutoff:3.500A)
      Proline residue:  B 410  - end of helix
      removed outlier: 3.934A  pdb=" N   ARG B 414 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 422 " --> pdb=" O   CYS B 418 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 428 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE B 432 " --> pdb=" O   PHE B 428 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 456
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.717A  pdb=" N   THR B 463 " --> pdb=" O   ASP B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 492
    Processing helix  chain 'B' and resid 492 through 514
    Processing helix  chain 'B' and resid 519 through 526
    Processing helix  chain 'C' and resid 34 through 47
    Processing helix  chain 'C' and resid 49 through 56
      removed outlier: 3.771A  pdb=" N   PHE C  53 " --> pdb=" O   PRO C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 103
      removed outlier: 3.823A  pdb=" N   ALA C  64 " --> pdb=" O   PRO C  60 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN C  66 " --> pdb=" O   LYS C  62 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLU C  93 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 135
    Processing helix  chain 'C' and resid 135 through 140
    Processing helix  chain 'C' and resid 226 through 233
      removed outlier: 3.935A  pdb=" N   VAL C 230 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   HIS C 232 " --> pdb=" O   GLN C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 324
      removed outlier: 4.150A  pdb=" N   PHE C 288 " --> pdb=" O   TYR C 284 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA C 290 " --> pdb=" O   MET C 286 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 338
      removed outlier: 3.602A  pdb=" N   VAL C 338 " --> pdb=" O   GLN C 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 366
      removed outlier: 3.894A  pdb=" N   MET C 344 " --> pdb=" O   GLY C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 395
      removed outlier: 4.305A  pdb=" N   ILE C 389 " --> pdb=" O   TRP C 385 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG C 390 " --> pdb=" O   LEU C 386 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   PHE C 394 " --> pdb=" O   ARG C 390 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE C 395 " --> pdb=" O   TYR C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 435
      removed outlier: 4.337A  pdb=" N   LEU C 401 " --> pdb=" O   LYS C 397 " (cutoff:3.500A)
      Proline residue:  C 410  - end of helix
      removed outlier: 3.934A  pdb=" N   ARG C 414 " --> pdb=" O   PRO C 410 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE C 422 " --> pdb=" O   CYS C 418 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE C 428 " --> pdb=" O   LEU C 424 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE C 432 " --> pdb=" O   PHE C 428 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 443 through 456
    Processing helix  chain 'C' and resid 459 through 466
      removed outlier: 3.717A  pdb=" N   THR C 463 " --> pdb=" O   ASP C 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 471 through 492
    Processing helix  chain 'C' and resid 492 through 514
    Processing helix  chain 'C' and resid 519 through 526
    Processing helix  chain 'D' and resid 34 through 47
    Processing helix  chain 'D' and resid 49 through 56
      removed outlier: 3.770A  pdb=" N   PHE D  53 " --> pdb=" O   PRO D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 103
      removed outlier: 3.822A  pdb=" N   ALA D  64 " --> pdb=" O   PRO D  60 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN D  66 " --> pdb=" O   LYS D  62 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLU D  93 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 135
    Processing helix  chain 'D' and resid 135 through 140
    Processing helix  chain 'D' and resid 226 through 233
      removed outlier: 3.935A  pdb=" N   VAL D 230 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   HIS D 232 " --> pdb=" O   GLN D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 324
      removed outlier: 4.150A  pdb=" N   PHE D 288 " --> pdb=" O   TYR D 284 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ALA D 290 " --> pdb=" O   MET D 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 338
      removed outlier: 3.602A  pdb=" N   VAL D 338 " --> pdb=" O   GLN D 334 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 340 through 366
      removed outlier: 3.894A  pdb=" N   MET D 344 " --> pdb=" O   GLY D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 395
      removed outlier: 4.304A  pdb=" N   ILE D 389 " --> pdb=" O   TRP D 385 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ARG D 390 " --> pdb=" O   LEU D 386 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   PHE D 394 " --> pdb=" O   ARG D 390 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   PHE D 395 " --> pdb=" O   TYR D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 397 through 435
      removed outlier: 4.335A  pdb=" N   LEU D 401 " --> pdb=" O   LYS D 397 " (cutoff:3.500A)
      Proline residue:  D 410  - end of helix
      removed outlier: 3.934A  pdb=" N   ARG D 414 " --> pdb=" O   PRO D 410 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE D 422 " --> pdb=" O   CYS D 418 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   PHE D 428 " --> pdb=" O   LEU D 424 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE D 432 " --> pdb=" O   PHE D 428 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 443 through 456
    Processing helix  chain 'D' and resid 459 through 466
      removed outlier: 3.717A  pdb=" N   THR D 463 " --> pdb=" O   ASP D 459 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 471 through 492
    Processing helix  chain 'D' and resid 492 through 514
    Processing helix  chain 'D' and resid 519 through 526
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116
      removed outlier: 7.250A  pdb=" N   LEU A 213 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR A 163 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 215 " --> pdb=" O   HIS A 161 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169
      removed outlier: 3.565A  pdb=" N   ASN A 167 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   PHE A 175 " --> pdb=" O   HIS D 273 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274
      removed outlier: 3.607A  pdb=" N   PHE B 175 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN B 167 " --> pdb=" O   ASP B 176 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 116
      removed outlier: 7.251A  pdb=" N   LEU B 213 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR B 163 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 215 " --> pdb=" O   HIS B 161 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 271 through 274
      removed outlier: 3.589A  pdb=" N   PHE C 175 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN C 167 " --> pdb=" O   ASP C 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 116
      removed outlier: 7.250A  pdb=" N   LEU C 213 " --> pdb=" O   TYR C 163 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   TYR C 163 " --> pdb=" O   LEU C 213 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR C 215 " --> pdb=" O   HIS C 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 274
      removed outlier: 3.594A  pdb=" N   PHE D 175 " --> pdb=" O   ASP C 271 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN D 167 " --> pdb=" O   ASP D 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 115 through 116
      removed outlier: 7.250A  pdb=" N   LEU D 213 " --> pdb=" O   TYR D 163 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TYR D 163 " --> pdb=" O   LEU D 213 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR D 215 " --> pdb=" O   HIS D 161 " (cutoff:3.500A)

    1063 hydrogen bonds defined for protein.
    3141 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: 2.39

  Time building geometry restraints manager: 1.52 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: 4725
        1.34 -     1.47: 4182
        1.47 -     1.59: 6913
        1.59 -     1.72: 8
        1.72 -     1.85: 200
  Bond restraints: 16028
  Sorted by residual:
  bond pdb=" C   THR C 519 "
       pdb=" N   GLU C 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.253  0.081 1.27e-02 6.20e+03 4.11e+01
  bond pdb=" C   THR D 519 "
       pdb=" N   GLU D 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.253  0.081 1.27e-02 6.20e+03 4.11e+01
  bond pdb=" C   THR A 519 "
       pdb=" N   GLU A 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.253  0.081 1.27e-02 6.20e+03 4.10e+01
  bond pdb=" C   THR B 519 "
       pdb=" N   GLU B 520 "
    ideal  model  delta    sigma   weight residual
    1.334  1.254  0.080 1.27e-02 6.20e+03 4.02e+01
  bond pdb=" CB  ASP C  36 "
       pdb=" CG  ASP C  36 "
    ideal  model  delta    sigma   weight residual
    1.516  1.597 -0.081 2.50e-02 1.60e+03 1.04e+01
  ... (remaining 16023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.63: 21203
        3.63 -     7.25: 413
        7.25 -    10.88: 40
       10.88 -    14.51: 8
       14.51 -    18.13: 4
  Bond angle restraints: 21668
  Sorted by residual:
  angle pdb=" N   ARG B  58 "
        pdb=" CA  ARG B  58 "
        pdb=" C   ARG B  58 "
      ideal   model   delta    sigma   weight residual
     112.94  120.27   -7.33 1.41e+00 5.03e-01 2.70e+01
  angle pdb=" N   ARG A  58 "
        pdb=" CA  ARG A  58 "
        pdb=" C   ARG A  58 "
      ideal   model   delta    sigma   weight residual
     112.94  120.25   -7.31 1.41e+00 5.03e-01 2.69e+01
  angle pdb=" CA  LEU B 401 "
        pdb=" CB  LEU B 401 "
        pdb=" CG  LEU B 401 "
      ideal   model   delta    sigma   weight residual
     116.30  134.43  -18.13 3.50e+00 8.16e-02 2.68e+01
  angle pdb=" CA  LEU D 401 "
        pdb=" CB  LEU D 401 "
        pdb=" CG  LEU D 401 "
      ideal   model   delta    sigma   weight residual
     116.30  134.42  -18.12 3.50e+00 8.16e-02 2.68e+01
  angle pdb=" CA  LEU A 401 "
        pdb=" CB  LEU A 401 "
        pdb=" CG  LEU A 401 "
      ideal   model   delta    sigma   weight residual
     116.30  134.42  -18.12 3.50e+00 8.16e-02 2.68e+01
  ... (remaining 21663 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 8160
       16.02 -    32.03: 992
       32.03 -    48.05: 208
       48.05 -    64.07: 60
       64.07 -    80.09: 20
  Dihedral angle restraints: 9440
    sinusoidal: 3796
      harmonic: 5644
  Sorted by residual:
  dihedral pdb=" CA  GLY C 166 "
           pdb=" C   GLY C 166 "
           pdb=" N   ASN C 167 "
           pdb=" CA  ASN C 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.84   35.16     0      5.00e+00 4.00e-02 4.94e+01
  dihedral pdb=" CA  GLY A 166 "
           pdb=" C   GLY A 166 "
           pdb=" N   ASN A 167 "
           pdb=" CA  ASN A 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.84   35.16     0      5.00e+00 4.00e-02 4.94e+01
  dihedral pdb=" CA  GLY D 166 "
           pdb=" C   GLY D 166 "
           pdb=" N   ASN D 167 "
           pdb=" CA  ASN D 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.86   35.14     0      5.00e+00 4.00e-02 4.94e+01
  ... (remaining 9437 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 2152
       0.086 -    0.173: 276
       0.173 -    0.259: 20
       0.259 -    0.345: 0
       0.345 -    0.432: 4
  Chirality restraints: 2452
  Sorted by residual:
  chirality pdb=" CA  ARG A  58 "
            pdb=" N   ARG A  58 "
            pdb=" C   ARG A  58 "
            pdb=" CB  ARG A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.66e+00
  chirality pdb=" CA  ARG B  58 "
            pdb=" N   ARG B  58 "
            pdb=" C   ARG B  58 "
            pdb=" CB  ARG B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.65e+00
  chirality pdb=" CA  ARG C  58 "
            pdb=" N   ARG C  58 "
            pdb=" C   ARG C  58 "
            pdb=" CB  ARG C  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.59e+00
  ... (remaining 2449 not shown)

  Planarity restraints: 2668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  45 "    0.028 2.00e-02 2.50e+03   2.17e-02 8.24e+00
        pdb=" CG  PHE C  45 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  45 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  45 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  45 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  45 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  45 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  45 "    0.028 2.00e-02 2.50e+03   2.17e-02 8.23e+00
        pdb=" CG  PHE D  45 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  45 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  45 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  45 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  45 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  45 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  45 "   -0.028 2.00e-02 2.50e+03   2.16e-02 8.13e+00
        pdb=" CG  PHE A  45 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  45 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  45 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  45 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  45 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 2665 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 903
        2.72 -     3.27: 16526
        3.27 -     3.81: 24602
        3.81 -     4.36: 30260
        4.36 -     4.90: 50586
  Nonbonded interactions: 122877
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 176 "
            pdb=" OD1 ASP A 176 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ASP B 176 "
            pdb=" OD1 ASP B 176 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ASP C 176 "
            pdb=" OD1 ASP C 176 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ASP D 176 "
            pdb=" OD1 ASP D 176 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER A 330 "
            pdb=" CB  GLN A 334 "
     model   vdw
     2.221 2.752
  ... (remaining 122872 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.500
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.103  16028  Z= 0.382
  Angle     :  1.233  18.135  21668  Z= 0.669
  Chirality :  0.060   0.432   2452
  Planarity :  0.006   0.048   2668
  Dihedral  : 15.258  80.085   5784
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  5.56 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 16.44 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.22 %

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: -3.48 (0.16), residues: 1872
  helix: -2.45 (0.12), residues: 1112
  sheet: -0.16 (0.31), residues: 260
  loop : -2.61 (0.23), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.005   ARG D 390 
 TYR   0.041   0.004   TYR B 117 
 PHE   0.049   0.004   PHE C  45 
 TRP   0.026   0.004   TRP C 341 
 HIS   0.005   0.001   HIS C 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00828 (16028)
  covalent geometry    : angle       1.23320 (21668)
  hydrogen bonds       : bond        0.12322 ( 1063)
  hydrogen bonds       : angle       9.10682 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  676 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 664
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 PHE cc_start: 0.9440 (t80) cc_final: 0.8828 (t80)
REVERT: A   47 MET cc_start: 0.8892 (mtm) cc_final: 0.8502 (mtp)
REVERT: A   52 LYS cc_start: 0.8780 (mttt) cc_final: 0.8105 (mmtt)
REVERT: A   54 TRP cc_start: 0.7720 (t60) cc_final: 0.6853 (t-100)
REVERT: A   66 GLN cc_start: 0.8965 (mm110) cc_final: 0.7754 (mm110)
REVERT: A   69 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8617 (ttpp)
REVERT: A  124 ASP cc_start: 0.9020 (t0) cc_final: 0.8698 (t0)
REVERT: A  137 TYR cc_start: 0.8912 (m-80) cc_final: 0.8705 (m-80)
REVERT: A  271 ASP cc_start: 0.7982 (m-30) cc_final: 0.7766 (p0)
REVERT: A  286 MET cc_start: 0.8959 (mmm) cc_final: 0.8148 (ptm)
REVERT: A  312 GLN cc_start: 0.7668 (mt0) cc_final: 0.7320 (pt0)
REVERT: A  339 ASN cc_start: 0.8152 (t0) cc_final: 0.7916 (t0)
REVERT: A  341 TRP cc_start: 0.8535 (m100) cc_final: 0.8133 (m100)
REVERT: A  347 ILE cc_start: 0.9171 (mt) cc_final: 0.8886 (tp)
REVERT: A  361 GLU cc_start: 0.8840 (tt0) cc_final: 0.8035 (tp30)
REVERT: A  362 ILE cc_start: 0.9367 (mt) cc_final: 0.9133 (mm)
REVERT: A  382 MET cc_start: 0.9061 (ttp) cc_final: 0.8631 (tmm)
REVERT: A  409 LEU cc_start: 0.9081 (tp) cc_final: 0.8873 (tt)
REVERT: A  415 PHE cc_start: 0.9029 (t80) cc_final: 0.8448 (t80)
REVERT: A  443 SER cc_start: 0.9282 (p) cc_final: 0.9013 (t)
REVERT: A  459 ASP cc_start: 0.9210 (m-30) cc_final: 0.9003 (t0)
REVERT: A  512 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8936 (tm-30)
REVERT: B   44 PHE cc_start: 0.8410 (t80) cc_final: 0.8207 (t80)
REVERT: B   45 PHE cc_start: 0.9388 (t80) cc_final: 0.8752 (t80)
REVERT: B   47 MET cc_start: 0.9003 (mtm) cc_final: 0.8713 (mtp)
REVERT: B   54 TRP cc_start: 0.7447 (t60) cc_final: 0.6102 (t60)
REVERT: B   59 LYS cc_start: 0.6074 (ttmt) cc_final: 0.4809 (tppt)
REVERT: B   69 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8703 (ttpt)
REVERT: B   72 MET cc_start: 0.9399 (mmm) cc_final: 0.9171 (tpp)
REVERT: B  124 ASP cc_start: 0.9014 (t0) cc_final: 0.8692 (t0)
REVERT: B  186 PHE cc_start: 0.7658 (m-80) cc_final: 0.7364 (m-10)
REVERT: B  271 ASP cc_start: 0.8075 (m-30) cc_final: 0.7772 (p0)
REVERT: B  286 MET cc_start: 0.8965 (mmm) cc_final: 0.8234 (ptm)
REVERT: B  333 ASP cc_start: 0.7309 (m-30) cc_final: 0.6976 (m-30)
REVERT: B  347 ILE cc_start: 0.9210 (mt) cc_final: 0.8968 (tp)
REVERT: B  361 GLU cc_start: 0.8930 (tt0) cc_final: 0.8266 (tp30)
REVERT: B  382 MET cc_start: 0.9062 (ttp) cc_final: 0.8589 (tmm)
REVERT: B  383 LEU cc_start: 0.9216 (mp) cc_final: 0.8834 (mt)
REVERT: B  415 PHE cc_start: 0.9024 (t80) cc_final: 0.8381 (t80)
REVERT: B  443 SER cc_start: 0.9340 (p) cc_final: 0.8990 (t)
REVERT: B  454 LEU cc_start: 0.9386 (tp) cc_final: 0.9137 (tp)
REVERT: B  459 ASP cc_start: 0.9129 (m-30) cc_final: 0.8908 (t0)
REVERT: B  470 LYS cc_start: 0.8810 (mttt) cc_final: 0.8487 (mtmm)
REVERT: C   45 PHE cc_start: 0.9384 (t80) cc_final: 0.8742 (t80)
REVERT: C   47 MET cc_start: 0.9000 (mtm) cc_final: 0.8683 (mtp)
REVERT: C   52 LYS cc_start: 0.8736 (mttt) cc_final: 0.8099 (mmtt)
REVERT: C   54 TRP cc_start: 0.7524 (t60) cc_final: 0.6191 (t60)
REVERT: C   59 LYS cc_start: 0.6057 (ttmt) cc_final: 0.4824 (tppt)
REVERT: C   72 MET cc_start: 0.9375 (mmm) cc_final: 0.9108 (tpp)
REVERT: C   75 ILE cc_start: 0.9218 (mt) cc_final: 0.8999 (tt)
REVERT: C  124 ASP cc_start: 0.9007 (t0) cc_final: 0.8693 (t0)
REVERT: C  271 ASP cc_start: 0.8076 (m-30) cc_final: 0.7801 (p0)
REVERT: C  286 MET cc_start: 0.8965 (mmm) cc_final: 0.8244 (ptm)
REVERT: C  333 ASP cc_start: 0.7419 (m-30) cc_final: 0.7134 (m-30)
REVERT: C  347 ILE cc_start: 0.9208 (mt) cc_final: 0.8998 (tp)
REVERT: C  361 GLU cc_start: 0.8933 (tt0) cc_final: 0.8170 (tp30)
REVERT: C  362 ILE cc_start: 0.9382 (mt) cc_final: 0.9171 (mm)
REVERT: C  382 MET cc_start: 0.9042 (ttp) cc_final: 0.8570 (tmm)
REVERT: C  383 LEU cc_start: 0.9199 (mp) cc_final: 0.8820 (mt)
REVERT: C  415 PHE cc_start: 0.9009 (t80) cc_final: 0.8341 (t80)
REVERT: C  443 SER cc_start: 0.9341 (p) cc_final: 0.9001 (t)
REVERT: C  454 LEU cc_start: 0.9380 (tp) cc_final: 0.9138 (tp)
REVERT: C  459 ASP cc_start: 0.9081 (m-30) cc_final: 0.8877 (t0)
REVERT: C  470 LYS cc_start: 0.8760 (mttt) cc_final: 0.8427 (mtmm)
REVERT: D   45 PHE cc_start: 0.9419 (t80) cc_final: 0.8867 (t80)
REVERT: D   47 MET cc_start: 0.9016 (mtm) cc_final: 0.8697 (mtp)
REVERT: D   52 LYS cc_start: 0.8794 (mttt) cc_final: 0.7986 (mmtt)
REVERT: D   54 TRP cc_start: 0.7766 (t60) cc_final: 0.6441 (t60)
REVERT: D   59 LYS cc_start: 0.6194 (ttmt) cc_final: 0.4802 (tppt)
REVERT: D   66 GLN cc_start: 0.8921 (mm110) cc_final: 0.8607 (mm-40)
REVERT: D   72 MET cc_start: 0.9360 (mmm) cc_final: 0.9143 (tpp)
REVERT: D   79 LEU cc_start: 0.9619 (tp) cc_final: 0.9399 (mt)
REVERT: D  124 ASP cc_start: 0.9013 (t0) cc_final: 0.8689 (t0)
REVERT: D  271 ASP cc_start: 0.8015 (m-30) cc_final: 0.7700 (p0)
REVERT: D  286 MET cc_start: 0.8964 (mmm) cc_final: 0.8214 (ptm)
REVERT: D  344 MET cc_start: 0.8830 (mmm) cc_final: 0.8612 (mmt)
REVERT: D  347 ILE cc_start: 0.9225 (mt) cc_final: 0.8965 (tp)
REVERT: D  361 GLU cc_start: 0.8890 (tt0) cc_final: 0.8050 (tp30)
REVERT: D  362 ILE cc_start: 0.9403 (mt) cc_final: 0.9168 (mm)
REVERT: D  382 MET cc_start: 0.9043 (ttp) cc_final: 0.8534 (tmm)
REVERT: D  383 LEU cc_start: 0.9206 (mp) cc_final: 0.8845 (mt)
REVERT: D  415 PHE cc_start: 0.9043 (t80) cc_final: 0.8402 (t80)
REVERT: D  443 SER cc_start: 0.9381 (p) cc_final: 0.9062 (t)
REVERT: D  454 LEU cc_start: 0.9380 (tp) cc_final: 0.9155 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 664
  average time/residue: 0.1003
  time to fit residues: 101.6922
Evaluate side-chains
  418 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 410
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN
A 125 GLN
A 219 GLN
A 262 ASN
A 456 ASN
A 468 GLN
B 125 GLN
B 219 GLN
B 456 ASN
C 125 GLN
C 219 GLN
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 HIS
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 GLN
D 219 GLN
D 456 ASN
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.176629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.135983 restraints weight = 20689.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.139209 restraints weight = 13291.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.141314 restraints weight = 9928.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.142754 restraints weight = 8337.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.143225 restraints weight = 7486.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  16028  Z= 0.177
  Angle     :  0.683   9.570  21668  Z= 0.363
  Chirality :  0.045   0.229   2452
  Planarity :  0.004   0.040   2668
  Dihedral  :  5.360  26.237   2056
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  2.56 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.08 %
    Favored  : 95.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.53 (0.18), residues: 1872
  helix:  0.26 (0.14), residues: 1136
  sheet:  0.84 (0.33), residues: 220
  loop : -2.15 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 231 
 TYR   0.022   0.002   TYR D 391 
 PHE   0.021   0.002   PHE D 485 
 TRP   0.013   0.002   TRP D 475 
 HIS   0.007   0.002   HIS D 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (16028)
  covalent geometry    : angle       0.68280 (21668)
  hydrogen bonds       : bond        0.05625 ( 1063)
  hydrogen bonds       : angle       5.37414 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  620 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 609
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A   52 LYS cc_start: 0.8386 (mttt) cc_final: 0.8054 (mmtt)
REVERT: A   54 TRP cc_start: 0.5595 (t60) cc_final: 0.5373 (t-100)
REVERT: A  241 PHE cc_start: 0.8217 (m-10) cc_final: 0.7676 (m-10)
REVERT: A  273 HIS cc_start: 0.6984 (m90) cc_final: 0.6703 (m170)
REVERT: A  288 PHE cc_start: 0.9027 (t80) cc_final: 0.8729 (t80)
REVERT: A  301 ILE cc_start: 0.9115 (mt) cc_final: 0.8896 (mm)
REVERT: A  327 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7733 (mmtt)
REVERT: A  341 TRP cc_start: 0.8010 (m100) cc_final: 0.7421 (m100)
REVERT: A  375 ILE cc_start: 0.9194 (mt) cc_final: 0.8978 (mt)
REVERT: A  421 MET cc_start: 0.8329 (mmt) cc_final: 0.8113 (mmt)
REVERT: A  443 SER cc_start: 0.9042 (p) cc_final: 0.8771 (t)
REVERT: A  458 ASP cc_start: 0.8560 (t70) cc_final: 0.8100 (t0)
REVERT: A  460 MET cc_start: 0.7683 (ttp) cc_final: 0.7371 (ttp)
REVERT: A  498 ILE cc_start: 0.8788 (tt) cc_final: 0.8566 (tt)
REVERT: B   52 LYS cc_start: 0.8409 (mttt) cc_final: 0.8000 (mmtt)
REVERT: B   72 MET cc_start: 0.8811 (mmm) cc_final: 0.8509 (mmp)
REVERT: B  124 ASP cc_start: 0.8291 (t0) cc_final: 0.8079 (t0)
REVERT: B  241 PHE cc_start: 0.8226 (m-10) cc_final: 0.7674 (m-10)
REVERT: B  256 ILE cc_start: 0.9290 (mm) cc_final: 0.9031 (mt)
REVERT: B  288 PHE cc_start: 0.8963 (t80) cc_final: 0.8460 (t80)
REVERT: B  333 ASP cc_start: 0.5912 (m-30) cc_final: 0.5531 (m-30)
REVERT: B  375 ILE cc_start: 0.9182 (mt) cc_final: 0.8908 (mt)
REVERT: B  415 PHE cc_start: 0.7919 (t80) cc_final: 0.7333 (t80)
REVERT: B  443 SER cc_start: 0.9026 (p) cc_final: 0.8689 (t)
REVERT: B  458 ASP cc_start: 0.8523 (t70) cc_final: 0.8251 (t70)
REVERT: B  460 MET cc_start: 0.8044 (ttp) cc_final: 0.7815 (ttm)
REVERT: B  491 TYR cc_start: 0.8424 (m-10) cc_final: 0.8119 (m-10)
REVERT: B  521 LEU cc_start: 0.7760 (mp) cc_final: 0.7129 (mp)
REVERT: C   38 MET cc_start: 0.7291 (mmt) cc_final: 0.6559 (mmm)
REVERT: C   44 PHE cc_start: 0.8879 (t80) cc_final: 0.8238 (t80)
REVERT: C   52 LYS cc_start: 0.8472 (mttt) cc_final: 0.7938 (mmtt)
REVERT: C   72 MET cc_start: 0.8844 (mmm) cc_final: 0.8484 (tpp)
REVERT: C   93 GLU cc_start: 0.8042 (tp30) cc_final: 0.7797 (tp30)
REVERT: C  124 ASP cc_start: 0.8300 (t0) cc_final: 0.8091 (t0)
REVERT: C  241 PHE cc_start: 0.8257 (m-10) cc_final: 0.7719 (m-10)
REVERT: C  256 ILE cc_start: 0.9270 (mm) cc_final: 0.9042 (mt)
REVERT: C  333 ASP cc_start: 0.5952 (m-30) cc_final: 0.5609 (m-30)
REVERT: C  375 ILE cc_start: 0.9183 (mt) cc_final: 0.8920 (mt)
REVERT: C  415 PHE cc_start: 0.7882 (t80) cc_final: 0.7377 (t80)
REVERT: C  443 SER cc_start: 0.9012 (p) cc_final: 0.8710 (t)
REVERT: C  458 ASP cc_start: 0.8603 (t70) cc_final: 0.8182 (t70)
REVERT: C  460 MET cc_start: 0.7988 (ttp) cc_final: 0.7666 (ttm)
REVERT: C  491 TYR cc_start: 0.8447 (m-10) cc_final: 0.8233 (m-10)
REVERT: C  521 LEU cc_start: 0.7768 (mp) cc_final: 0.7284 (mp)
REVERT: D   44 PHE cc_start: 0.8974 (t80) cc_final: 0.8319 (t80)
REVERT: D   52 LYS cc_start: 0.8412 (mttt) cc_final: 0.7999 (mmtt)
REVERT: D   72 MET cc_start: 0.8764 (mmm) cc_final: 0.8456 (mmp)
REVERT: D  241 PHE cc_start: 0.8224 (m-10) cc_final: 0.7736 (m-10)
REVERT: D  256 ILE cc_start: 0.9281 (mm) cc_final: 0.9050 (mt)
REVERT: D  288 PHE cc_start: 0.8992 (t80) cc_final: 0.8537 (t80)
REVERT: D  375 ILE cc_start: 0.9151 (mt) cc_final: 0.8884 (mt)
REVERT: D  382 MET cc_start: 0.7907 (ttp) cc_final: 0.7664 (tmm)
REVERT: D  415 PHE cc_start: 0.7999 (t80) cc_final: 0.7527 (t80)
REVERT: D  421 MET cc_start: 0.8094 (mmt) cc_final: 0.7888 (mmt)
REVERT: D  443 SER cc_start: 0.9024 (p) cc_final: 0.8723 (t)
REVERT: D  491 TYR cc_start: 0.8391 (m-10) cc_final: 0.8150 (m-10)
  outliers start: 11
  outliers final: 0
  residues processed: 610
  average time/residue: 0.1159
  time to fit residues: 110.1833
Evaluate side-chains
  394 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 394
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 159 optimal weight:   10.0000
   chunk 138 optimal weight:    0.7980
   chunk 154 optimal weight:   20.0000
   chunk 61 optimal weight:    6.9990
   chunk 134 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 125 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 130 optimal weight:    0.9980
   chunk 167 optimal weight:    6.9990
   chunk 120 optimal weight:    9.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 262 ASN
A 406 GLN
B 262 ASN
C 219 GLN
C 262 ASN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 468 GLN
D 232 HIS
D 262 ASN
** D 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.171608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.131047 restraints weight = 21132.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.134530 restraints weight = 12953.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.136404 restraints weight = 9490.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.138355 restraints weight = 7951.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.138983 restraints weight = 7052.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  16028  Z= 0.196
  Angle     :  0.671  10.765  21668  Z= 0.353
  Chirality :  0.044   0.197   2452
  Planarity :  0.003   0.023   2668
  Dihedral  :  4.868  26.348   2056
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  3.62 %
    Favored  : 95.80 %
  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:  0.73 (0.19), residues: 1872
  helix:  1.33 (0.15), residues: 1132
  sheet:  1.28 (0.34), residues: 216
  loop : -1.76 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 231 
 TYR   0.020   0.002   TYR C 481 
 PHE   0.022   0.002   PHE A 485 
 TRP   0.010   0.001   TRP B  54 
 HIS   0.005   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (16028)
  covalent geometry    : angle       0.67073 (21668)
  hydrogen bonds       : bond        0.05349 ( 1063)
  hydrogen bonds       : angle       5.03212 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 474
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LYS cc_start: 0.8389 (mttt) cc_final: 0.7769 (mmtt)
REVERT: A   93 GLU cc_start: 0.8500 (tp30) cc_final: 0.8192 (tp30)
REVERT: A  273 HIS cc_start: 0.6910 (m90) cc_final: 0.6605 (m170)
REVERT: A  341 TRP cc_start: 0.7847 (m100) cc_final: 0.7498 (m100)
REVERT: A  361 GLU cc_start: 0.7307 (tp30) cc_final: 0.7057 (tp30)
REVERT: A  415 PHE cc_start: 0.8043 (t80) cc_final: 0.7558 (t80)
REVERT: A  423 TYR cc_start: 0.8343 (t80) cc_final: 0.8075 (t80)
REVERT: A  443 SER cc_start: 0.8985 (p) cc_final: 0.8712 (t)
REVERT: A  449 GLU cc_start: 0.7658 (pt0) cc_final: 0.7428 (pt0)
REVERT: A  458 ASP cc_start: 0.8754 (t70) cc_final: 0.8380 (t0)
REVERT: A  524 PHE cc_start: 0.7738 (t80) cc_final: 0.7380 (t80)
REVERT: B   44 PHE cc_start: 0.8888 (t80) cc_final: 0.7924 (t80)
REVERT: B   72 MET cc_start: 0.8697 (mmm) cc_final: 0.8308 (mmp)
REVERT: B   93 GLU cc_start: 0.8402 (tp30) cc_final: 0.8133 (tp30)
REVERT: B  288 PHE cc_start: 0.8897 (t80) cc_final: 0.8117 (t80)
REVERT: B  327 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7643 (mmtt)
REVERT: B  415 PHE cc_start: 0.7969 (t80) cc_final: 0.7422 (t80)
REVERT: B  423 TYR cc_start: 0.8453 (t80) cc_final: 0.8167 (t80)
REVERT: B  443 SER cc_start: 0.8975 (p) cc_final: 0.8738 (t)
REVERT: B  458 ASP cc_start: 0.8725 (t70) cc_final: 0.8240 (t70)
REVERT: B  491 TYR cc_start: 0.8309 (m-10) cc_final: 0.8105 (m-10)
REVERT: B  521 LEU cc_start: 0.8332 (mp) cc_final: 0.8005 (mp)
REVERT: C   44 PHE cc_start: 0.8842 (t80) cc_final: 0.7844 (t80)
REVERT: C   72 MET cc_start: 0.8781 (mmm) cc_final: 0.8378 (tpp)
REVERT: C  294 LEU cc_start: 0.9056 (mp) cc_final: 0.8851 (mp)
REVERT: C  347 ILE cc_start: 0.9275 (tp) cc_final: 0.8947 (tt)
REVERT: C  415 PHE cc_start: 0.7876 (t80) cc_final: 0.7376 (t80)
REVERT: C  423 TYR cc_start: 0.8492 (t80) cc_final: 0.8163 (t80)
REVERT: C  443 SER cc_start: 0.8990 (p) cc_final: 0.8751 (t)
REVERT: C  458 ASP cc_start: 0.8736 (t70) cc_final: 0.8292 (t70)
REVERT: C  521 LEU cc_start: 0.8346 (mp) cc_final: 0.7980 (mp)
REVERT: D   44 PHE cc_start: 0.8924 (t80) cc_final: 0.7949 (t80)
REVERT: D   72 MET cc_start: 0.8649 (mmm) cc_final: 0.8336 (mmp)
REVERT: D   93 GLU cc_start: 0.8434 (tp30) cc_final: 0.8121 (tp30)
REVERT: D  288 PHE cc_start: 0.8909 (t80) cc_final: 0.8237 (t80)
REVERT: D  335 MET cc_start: 0.6284 (mmm) cc_final: 0.5747 (mtm)
REVERT: D  361 GLU cc_start: 0.7375 (tp30) cc_final: 0.7075 (tp30)
REVERT: D  415 PHE cc_start: 0.7964 (t80) cc_final: 0.7435 (t80)
REVERT: D  423 TYR cc_start: 0.8406 (t80) cc_final: 0.8044 (t80)
REVERT: D  443 SER cc_start: 0.8991 (p) cc_final: 0.8749 (t)
  outliers start: 10
  outliers final: 0
  residues processed: 475
  average time/residue: 0.1138
  time to fit residues: 84.3743
Evaluate side-chains
  361 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 361
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 140 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 120 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 153 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   chunk 131 optimal weight:    0.6980
   chunk 177 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
B 468 GLN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 GLN
D 468 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.173990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.133633 restraints weight = 20939.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.137201 restraints weight = 12814.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.139434 restraints weight = 9329.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.141094 restraints weight = 7696.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.141475 restraints weight = 6876.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.5217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  16028  Z= 0.161
  Angle     :  0.605   9.491  21668  Z= 0.323
  Chirality :  0.042   0.187   2452
  Planarity :  0.003   0.023   2668
  Dihedral  :  4.660  24.882   2056
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.11 (0.19), residues: 1872
  helix:  1.73 (0.15), residues: 1140
  sheet:  1.25 (0.32), residues: 224
  loop : -1.88 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 231 
 TYR   0.021   0.002   TYR D 481 
 PHE   0.036   0.002   PHE B 489 
 TRP   0.009   0.001   TRP D 341 
 HIS   0.005   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (16028)
  covalent geometry    : angle       0.60490 (21668)
  hydrogen bonds       : bond        0.04925 ( 1063)
  hydrogen bonds       : angle       4.69206 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  474 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 474
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A   52 LYS cc_start: 0.8200 (mttt) cc_final: 0.7650 (mmtt)
REVERT: A  156 MET cc_start: 0.9054 (tmm) cc_final: 0.8694 (tmm)
REVERT: A  341 TRP cc_start: 0.7865 (m100) cc_final: 0.7518 (m100)
REVERT: A  361 GLU cc_start: 0.7335 (tp30) cc_final: 0.7018 (tp30)
REVERT: A  415 PHE cc_start: 0.7981 (t80) cc_final: 0.7430 (t80)
REVERT: A  449 GLU cc_start: 0.7676 (pt0) cc_final: 0.7431 (pt0)
REVERT: A  458 ASP cc_start: 0.8792 (t70) cc_final: 0.8482 (t0)
REVERT: A  512 GLN cc_start: 0.8170 (tp40) cc_final: 0.7918 (tm-30)
REVERT: A  524 PHE cc_start: 0.7683 (t80) cc_final: 0.7162 (t80)
REVERT: B   44 PHE cc_start: 0.8871 (t80) cc_final: 0.8506 (t80)
REVERT: B   52 LYS cc_start: 0.8266 (mttt) cc_final: 0.7795 (mmtt)
REVERT: B   72 MET cc_start: 0.8684 (mmm) cc_final: 0.8369 (mmp)
REVERT: B  335 MET cc_start: 0.6005 (mmm) cc_final: 0.5049 (mtm)
REVERT: B  415 PHE cc_start: 0.8024 (t80) cc_final: 0.7345 (t80)
REVERT: B  458 ASP cc_start: 0.8766 (t70) cc_final: 0.8318 (t70)
REVERT: B  460 MET cc_start: 0.7615 (ttm) cc_final: 0.7390 (ttm)
REVERT: B  491 TYR cc_start: 0.8259 (m-10) cc_final: 0.8033 (m-10)
REVERT: C   44 PHE cc_start: 0.8842 (t80) cc_final: 0.8444 (t80)
REVERT: C   52 LYS cc_start: 0.8197 (mttt) cc_final: 0.7805 (mmtt)
REVERT: C   72 MET cc_start: 0.8704 (mmm) cc_final: 0.8316 (tpp)
REVERT: C  156 MET cc_start: 0.9041 (tmm) cc_final: 0.8696 (tmm)
REVERT: C  335 MET cc_start: 0.6420 (mmm) cc_final: 0.5954 (mtm)
REVERT: C  415 PHE cc_start: 0.7939 (t80) cc_final: 0.7377 (t80)
REVERT: C  458 ASP cc_start: 0.8760 (t70) cc_final: 0.8470 (t70)
REVERT: C  491 TYR cc_start: 0.8413 (m-10) cc_final: 0.8199 (m-10)
REVERT: C  512 GLN cc_start: 0.8107 (tt0) cc_final: 0.7834 (tm-30)
REVERT: D   44 PHE cc_start: 0.8819 (t80) cc_final: 0.8402 (t80)
REVERT: D   52 LYS cc_start: 0.8154 (mttt) cc_final: 0.7775 (mmtt)
REVERT: D   72 MET cc_start: 0.8657 (mmm) cc_final: 0.8346 (mmp)
REVERT: D  217 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7648 (mt-10)
REVERT: D  335 MET cc_start: 0.6296 (mmm) cc_final: 0.5759 (mtm)
REVERT: D  361 GLU cc_start: 0.7386 (tp30) cc_final: 0.7112 (tp30)
REVERT: D  415 PHE cc_start: 0.7882 (t80) cc_final: 0.7306 (t80)
REVERT: D  443 SER cc_start: 0.8899 (p) cc_final: 0.8660 (t)
REVERT: D  512 GLN cc_start: 0.8218 (tt0) cc_final: 0.7878 (tm-30)
REVERT: D  524 PHE cc_start: 0.7602 (t80) cc_final: 0.7299 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 474
  average time/residue: 0.1124
  time to fit residues: 82.4757
Evaluate side-chains
  352 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 352
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 127 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 175 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   chunk 182 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 137 optimal weight:    0.8980
   chunk 57 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.175989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.140135 restraints weight = 20907.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.141990 restraints weight = 12927.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.141997 restraints weight = 9657.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.142674 restraints weight = 9687.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.142805 restraints weight = 8718.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.5565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  16028  Z= 0.139
  Angle     :  0.587   8.562  21668  Z= 0.307
  Chirality :  0.041   0.168   2452
  Planarity :  0.003   0.021   2668
  Dihedral  :  4.446  22.315   2056
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.84 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.19), residues: 1872
  helix:  1.95 (0.15), residues: 1132
  sheet:  1.44 (0.32), residues: 216
  loop : -1.92 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 414 
 TYR   0.022   0.001   TYR A 481 
 PHE   0.026   0.002   PHE D 489 
 TRP   0.009   0.001   TRP B 341 
 HIS   0.005   0.001   HIS D 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (16028)
  covalent geometry    : angle       0.58654 (21668)
  hydrogen bonds       : bond        0.04584 ( 1063)
  hydrogen bonds       : angle       4.49801 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 469
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  294 LEU cc_start: 0.9163 (mp) cc_final: 0.8921 (mp)
REVERT: A  335 MET cc_start: 0.5980 (mmm) cc_final: 0.5332 (ptp)
REVERT: A  341 TRP cc_start: 0.7795 (m100) cc_final: 0.7475 (m100)
REVERT: A  391 TYR cc_start: 0.7101 (t80) cc_final: 0.6853 (t80)
REVERT: A  402 ILE cc_start: 0.9120 (mm) cc_final: 0.8767 (mm)
REVERT: A  415 PHE cc_start: 0.8017 (t80) cc_final: 0.7572 (t80)
REVERT: A  512 GLN cc_start: 0.8215 (tp40) cc_final: 0.7934 (tm-30)
REVERT: A  524 PHE cc_start: 0.7758 (t80) cc_final: 0.7157 (t80)
REVERT: B   72 MET cc_start: 0.8632 (mmm) cc_final: 0.8273 (tpp)
REVERT: B  294 LEU cc_start: 0.8987 (mp) cc_final: 0.8763 (mp)
REVERT: B  335 MET cc_start: 0.6078 (mmm) cc_final: 0.5353 (mtm)
REVERT: B  375 ILE cc_start: 0.9184 (mt) cc_final: 0.8980 (mt)
REVERT: B  391 TYR cc_start: 0.7031 (t80) cc_final: 0.6790 (t80)
REVERT: B  415 PHE cc_start: 0.8069 (t80) cc_final: 0.7300 (t80)
REVERT: B  458 ASP cc_start: 0.8673 (t70) cc_final: 0.8289 (t70)
REVERT: B  491 TYR cc_start: 0.8268 (m-10) cc_final: 0.8046 (m-10)
REVERT: C   72 MET cc_start: 0.8679 (mmm) cc_final: 0.8283 (tpp)
REVERT: C  325 TYR cc_start: 0.6447 (m-80) cc_final: 0.6024 (m-80)
REVERT: C  335 MET cc_start: 0.6236 (mmm) cc_final: 0.5911 (ptp)
REVERT: C  375 ILE cc_start: 0.9160 (mt) cc_final: 0.8960 (mt)
REVERT: C  415 PHE cc_start: 0.7928 (t80) cc_final: 0.7305 (t80)
REVERT: C  458 ASP cc_start: 0.8538 (t70) cc_final: 0.8338 (t70)
REVERT: D   72 MET cc_start: 0.8589 (mmm) cc_final: 0.8275 (tpp)
REVERT: D  217 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7604 (mt-10)
REVERT: D  335 MET cc_start: 0.6203 (mmm) cc_final: 0.5716 (mtm)
REVERT: D  375 ILE cc_start: 0.9211 (mt) cc_final: 0.8960 (mt)
REVERT: D  391 TYR cc_start: 0.7049 (t80) cc_final: 0.6806 (t80)
REVERT: D  415 PHE cc_start: 0.7994 (t80) cc_final: 0.7368 (t80)
REVERT: D  524 PHE cc_start: 0.7620 (t80) cc_final: 0.7310 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 469
  average time/residue: 0.1061
  time to fit residues: 77.4738
Evaluate side-chains
  365 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 365
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 125 optimal weight:    0.2980
   chunk 110 optimal weight:    6.9990
   chunk 123 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 115 optimal weight:    7.9990
   chunk 160 optimal weight:    4.9990
   chunk 166 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   chunk 147 optimal weight:    0.7980
   chunk 105 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
C 228 GLN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.177948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.139959 restraints weight = 20941.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.143127 restraints weight = 13240.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.145052 restraints weight = 9881.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.145997 restraints weight = 8356.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147186 restraints weight = 7609.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.5857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16028  Z= 0.131
  Angle     :  0.576   7.750  21668  Z= 0.306
  Chirality :  0.041   0.202   2452
  Planarity :  0.003   0.026   2668
  Dihedral  :  4.331  24.350   2056
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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:  1.53 (0.19), residues: 1872
  helix:  2.12 (0.15), residues: 1136
  sheet:  1.66 (0.32), residues: 216
  loop : -1.93 (0.24), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  39 
 TYR   0.027   0.001   TYR A 426 
 PHE   0.029   0.002   PHE C 489 
 TRP   0.009   0.001   TRP D 341 
 HIS   0.004   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (16028)
  covalent geometry    : angle       0.57591 (21668)
  hydrogen bonds       : bond        0.04338 ( 1063)
  hydrogen bonds       : angle       4.36703 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  465 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 465
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8941 (tmm) cc_final: 0.8708 (tmm)
REVERT: A  335 MET cc_start: 0.5953 (mmm) cc_final: 0.5494 (ptp)
REVERT: A  341 TRP cc_start: 0.7726 (m100) cc_final: 0.7416 (m100)
REVERT: A  375 ILE cc_start: 0.9153 (mt) cc_final: 0.8943 (mt)
REVERT: A  391 TYR cc_start: 0.7136 (t80) cc_final: 0.6902 (t80)
REVERT: A  415 PHE cc_start: 0.7918 (t80) cc_final: 0.7589 (t80)
REVERT: A  460 MET cc_start: 0.7675 (ttm) cc_final: 0.7376 (ttm)
REVERT: A  512 GLN cc_start: 0.8191 (tp40) cc_final: 0.7901 (tm-30)
REVERT: B   52 LYS cc_start: 0.7855 (mttt) cc_final: 0.7491 (mmtt)
REVERT: B   72 MET cc_start: 0.8518 (mmm) cc_final: 0.8221 (tpp)
REVERT: B  335 MET cc_start: 0.6324 (mmm) cc_final: 0.5690 (mtm)
REVERT: B  388 VAL cc_start: 0.9195 (t) cc_final: 0.8924 (t)
REVERT: B  415 PHE cc_start: 0.8068 (t80) cc_final: 0.7204 (t80)
REVERT: B  458 ASP cc_start: 0.8408 (t70) cc_final: 0.8181 (t70)
REVERT: B  460 MET cc_start: 0.7314 (ttm) cc_final: 0.7082 (ttp)
REVERT: C   36 ASP cc_start: 0.5893 (m-30) cc_final: 0.5391 (t70)
REVERT: C   52 LYS cc_start: 0.7906 (mttt) cc_final: 0.7552 (mmtt)
REVERT: C   72 MET cc_start: 0.8566 (mmm) cc_final: 0.8233 (tpp)
REVERT: C  156 MET cc_start: 0.9056 (tmm) cc_final: 0.8751 (tmm)
REVERT: C  294 LEU cc_start: 0.9007 (mp) cc_final: 0.8805 (mp)
REVERT: C  335 MET cc_start: 0.6163 (mmm) cc_final: 0.5946 (mtt)
REVERT: C  375 ILE cc_start: 0.9154 (mt) cc_final: 0.8931 (mt)
REVERT: C  415 PHE cc_start: 0.8015 (t80) cc_final: 0.7244 (t80)
REVERT: D   52 LYS cc_start: 0.7903 (mttt) cc_final: 0.7556 (mmtt)
REVERT: D   72 MET cc_start: 0.8514 (mmm) cc_final: 0.8243 (tpp)
REVERT: D  335 MET cc_start: 0.6204 (mmm) cc_final: 0.5840 (mtm)
REVERT: D  415 PHE cc_start: 0.7921 (t80) cc_final: 0.7405 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 465
  average time/residue: 0.1087
  time to fit residues: 78.4438
Evaluate side-chains
  372 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 372
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 113 optimal weight:    6.9990
   chunk 185 optimal weight:    3.9990
   chunk 146 optimal weight:    5.9990
   chunk 184 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
C 228 GLN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.176219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.139197 restraints weight = 21018.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.141028 restraints weight = 13199.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141729 restraints weight = 10217.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.142214 restraints weight = 8916.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.142420 restraints weight = 8421.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.5985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  16028  Z= 0.142
  Angle     :  0.571   6.424  21668  Z= 0.305
  Chirality :  0.041   0.186   2452
  Planarity :  0.003   0.021   2668
  Dihedral  :  4.263  23.279   2056
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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:  1.48 (0.19), residues: 1872
  helix:  2.04 (0.15), residues: 1140
  sheet:  1.77 (0.33), residues: 216
  loop : -1.93 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 414 
 TYR   0.018   0.001   TYR D 481 
 PHE   0.030   0.002   PHE A 524 
 TRP   0.016   0.001   TRP D 341 
 HIS   0.006   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (16028)
  covalent geometry    : angle       0.57103 (21668)
  hydrogen bonds       : bond        0.04359 ( 1063)
  hydrogen bonds       : angle       4.35939 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  461 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 461
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.9025 (tmm) cc_final: 0.8702 (tmm)
REVERT: A  335 MET cc_start: 0.6080 (mmm) cc_final: 0.5827 (ptp)
REVERT: A  341 TRP cc_start: 0.7719 (m100) cc_final: 0.7472 (m100)
REVERT: A  388 VAL cc_start: 0.9189 (t) cc_final: 0.8907 (t)
REVERT: A  391 TYR cc_start: 0.7336 (t80) cc_final: 0.7044 (t80)
REVERT: A  415 PHE cc_start: 0.8050 (t80) cc_final: 0.7493 (t80)
REVERT: A  512 GLN cc_start: 0.8163 (tp40) cc_final: 0.7934 (tm-30)
REVERT: B   52 LYS cc_start: 0.8072 (mttt) cc_final: 0.7706 (mmtt)
REVERT: B   72 MET cc_start: 0.8576 (mmm) cc_final: 0.8363 (mmp)
REVERT: B  156 MET cc_start: 0.9099 (tmm) cc_final: 0.8842 (tmm)
REVERT: B  335 MET cc_start: 0.6208 (mmm) cc_final: 0.5852 (ptp)
REVERT: B  361 GLU cc_start: 0.7490 (tp30) cc_final: 0.7189 (tp30)
REVERT: B  415 PHE cc_start: 0.8238 (t80) cc_final: 0.7247 (t80)
REVERT: B  458 ASP cc_start: 0.8570 (t70) cc_final: 0.8264 (t70)
REVERT: B  492 MET cc_start: 0.7927 (tpp) cc_final: 0.7688 (tpp)
REVERT: C   36 ASP cc_start: 0.6101 (m-30) cc_final: 0.5567 (t70)
REVERT: C   52 LYS cc_start: 0.8066 (mttt) cc_final: 0.7722 (mmtt)
REVERT: C   72 MET cc_start: 0.8591 (mmm) cc_final: 0.8221 (tpp)
REVERT: C  110 MET cc_start: 0.5733 (ttm) cc_final: 0.5497 (ttm)
REVERT: C  156 MET cc_start: 0.9049 (tmm) cc_final: 0.8694 (tmm)
REVERT: C  375 ILE cc_start: 0.9181 (mt) cc_final: 0.8930 (mt)
REVERT: C  415 PHE cc_start: 0.8150 (t80) cc_final: 0.7244 (t80)
REVERT: C  460 MET cc_start: 0.7855 (ttm) cc_final: 0.7640 (ttm)
REVERT: C  512 GLN cc_start: 0.8320 (tp40) cc_final: 0.7839 (tm-30)
REVERT: D   52 LYS cc_start: 0.8197 (mttt) cc_final: 0.7805 (mmtt)
REVERT: D   72 MET cc_start: 0.8543 (mmm) cc_final: 0.8316 (mmp)
REVERT: D  335 MET cc_start: 0.6187 (mmm) cc_final: 0.5861 (mtm)
REVERT: D  415 PHE cc_start: 0.7991 (t80) cc_final: 0.7406 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 461
  average time/residue: 0.1098
  time to fit residues: 79.8071
Evaluate side-chains
  361 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 361
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 97 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 324 HIS
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.175367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.137170 restraints weight = 20918.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.140408 restraints weight = 13272.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.142289 restraints weight = 9874.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.143900 restraints weight = 8259.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.144210 restraints weight = 7391.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.6091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  16028  Z= 0.146
  Angle     :  0.581   7.496  21668  Z= 0.310
  Chirality :  0.042   0.184   2452
  Planarity :  0.003   0.020   2668
  Dihedral  :  4.291  24.833   2056
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  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:  1.53 (0.19), residues: 1872
  helix:  2.01 (0.15), residues: 1140
  sheet:  1.84 (0.33), residues: 216
  loop : -1.77 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 165 
 TYR   0.018   0.001   TYR C 426 
 PHE   0.022   0.002   PHE B 489 
 TRP   0.026   0.001   TRP B 341 
 HIS   0.003   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (16028)
  covalent geometry    : angle       0.58123 (21668)
  hydrogen bonds       : bond        0.04352 ( 1063)
  hydrogen bonds       : angle       4.36144 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 459
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.6581 (ttp) cc_final: 0.6351 (ptm)
REVERT: A  156 MET cc_start: 0.9018 (tmm) cc_final: 0.8712 (tmm)
REVERT: A  335 MET cc_start: 0.6186 (mmm) cc_final: 0.5839 (mtm)
REVERT: A  341 TRP cc_start: 0.7620 (m100) cc_final: 0.7415 (m100)
REVERT: A  391 TYR cc_start: 0.7288 (t80) cc_final: 0.6966 (t80)
REVERT: A  415 PHE cc_start: 0.8000 (t80) cc_final: 0.7491 (t80)
REVERT: B   52 LYS cc_start: 0.7797 (mttt) cc_final: 0.7569 (mmtt)
REVERT: B   72 MET cc_start: 0.8535 (mmm) cc_final: 0.8208 (mmp)
REVERT: B  156 MET cc_start: 0.9053 (tmm) cc_final: 0.8820 (tmm)
REVERT: B  335 MET cc_start: 0.6138 (mmm) cc_final: 0.5807 (ptp)
REVERT: B  388 VAL cc_start: 0.9101 (t) cc_final: 0.8891 (t)
REVERT: B  415 PHE cc_start: 0.8287 (t80) cc_final: 0.7367 (t80)
REVERT: B  458 ASP cc_start: 0.8511 (t70) cc_final: 0.8210 (t70)
REVERT: C   36 ASP cc_start: 0.5952 (m-30) cc_final: 0.5524 (t70)
REVERT: C   52 LYS cc_start: 0.7755 (mttt) cc_final: 0.7529 (mmtt)
REVERT: C   72 MET cc_start: 0.8518 (mmm) cc_final: 0.8199 (tpp)
REVERT: C  110 MET cc_start: 0.5677 (ttm) cc_final: 0.5413 (ttm)
REVERT: C  156 MET cc_start: 0.8953 (tmm) cc_final: 0.8684 (tmm)
REVERT: C  232 HIS cc_start: 0.5900 (m90) cc_final: 0.5592 (m90)
REVERT: C  361 GLU cc_start: 0.7438 (tp30) cc_final: 0.7214 (tp30)
REVERT: C  382 MET cc_start: 0.6799 (tmm) cc_final: 0.6481 (tpt)
REVERT: C  415 PHE cc_start: 0.8098 (t80) cc_final: 0.7230 (t80)
REVERT: C  458 ASP cc_start: 0.8632 (t70) cc_final: 0.8332 (t0)
REVERT: D   52 LYS cc_start: 0.8046 (mttt) cc_final: 0.7717 (mmtt)
REVERT: D   72 MET cc_start: 0.8528 (mmm) cc_final: 0.8263 (mmp)
REVERT: D  232 HIS cc_start: 0.5857 (m90) cc_final: 0.5522 (m90)
REVERT: D  335 MET cc_start: 0.6140 (mmm) cc_final: 0.5767 (mtm)
REVERT: D  382 MET cc_start: 0.7558 (tpt) cc_final: 0.7332 (tpp)
REVERT: D  415 PHE cc_start: 0.7993 (t80) cc_final: 0.7459 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 459
  average time/residue: 0.1097
  time to fit residues: 79.3007
Evaluate side-chains
  370 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 370
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 91 optimal weight:    0.4980
   chunk 171 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9990
   chunk 156 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 324 HIS
B 406 GLN
C 228 GLN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.179969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.141435 restraints weight = 20894.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.145018 restraints weight = 12698.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147375 restraints weight = 9159.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.148491 restraints weight = 7530.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.148969 restraints weight = 6783.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.6339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  16028  Z= 0.128
  Angle     :  0.575   7.735  21668  Z= 0.304
  Chirality :  0.041   0.195   2452
  Planarity :  0.003   0.020   2668
  Dihedral  :  4.283  21.905   2056
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.04 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.19), residues: 1872
  helix:  1.92 (0.15), residues: 1144
  sheet:  1.91 (0.33), residues: 216
  loop : -1.83 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 414 
 TYR   0.019   0.001   TYR D 481 
 PHE   0.026   0.002   PHE A 320 
 TRP   0.020   0.001   TRP B 341 
 HIS   0.010   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (16028)
  covalent geometry    : angle       0.57532 (21668)
  hydrogen bonds       : bond        0.04168 ( 1063)
  hydrogen bonds       : angle       4.37529 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 462
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8978 (tmm) cc_final: 0.8661 (tmm)
REVERT: A  285 MET cc_start: 0.8302 (mmm) cc_final: 0.7569 (mmt)
REVERT: A  301 ILE cc_start: 0.8882 (mt) cc_final: 0.8644 (mm)
REVERT: A  335 MET cc_start: 0.6138 (mmm) cc_final: 0.5747 (mtm)
REVERT: A  341 TRP cc_start: 0.7633 (m100) cc_final: 0.7409 (m100)
REVERT: A  391 TYR cc_start: 0.7192 (t80) cc_final: 0.6888 (t80)
REVERT: A  415 PHE cc_start: 0.7938 (t80) cc_final: 0.7289 (t80)
REVERT: A  491 TYR cc_start: 0.8571 (m-10) cc_final: 0.8252 (m-10)
REVERT: B   72 MET cc_start: 0.8485 (mmm) cc_final: 0.8239 (mmp)
REVERT: B  156 MET cc_start: 0.9054 (tmm) cc_final: 0.8779 (tmm)
REVERT: B  335 MET cc_start: 0.6034 (mmm) cc_final: 0.5760 (ptp)
REVERT: B  361 GLU cc_start: 0.7494 (tp30) cc_final: 0.7231 (tp30)
REVERT: B  375 ILE cc_start: 0.9318 (mt) cc_final: 0.9115 (mt)
REVERT: B  388 VAL cc_start: 0.9157 (t) cc_final: 0.8848 (t)
REVERT: B  415 PHE cc_start: 0.8270 (t80) cc_final: 0.7326 (t80)
REVERT: B  458 ASP cc_start: 0.8417 (t70) cc_final: 0.8075 (t70)
REVERT: C   36 ASP cc_start: 0.5923 (m-30) cc_final: 0.5531 (t70)
REVERT: C   72 MET cc_start: 0.8510 (mmm) cc_final: 0.8219 (tpp)
REVERT: C  110 MET cc_start: 0.5666 (ttm) cc_final: 0.5443 (ttm)
REVERT: C  120 SER cc_start: 0.8891 (p) cc_final: 0.8660 (p)
REVERT: C  156 MET cc_start: 0.8970 (tmm) cc_final: 0.8644 (tmm)
REVERT: C  232 HIS cc_start: 0.5816 (m90) cc_final: 0.5428 (m90)
REVERT: C  375 ILE cc_start: 0.9109 (mt) cc_final: 0.8862 (mt)
REVERT: C  382 MET cc_start: 0.6766 (tmm) cc_final: 0.6496 (tpt)
REVERT: C  388 VAL cc_start: 0.9136 (t) cc_final: 0.8931 (t)
REVERT: C  415 PHE cc_start: 0.8108 (t80) cc_final: 0.7189 (t80)
REVERT: C  439 ASP cc_start: 0.7768 (p0) cc_final: 0.7560 (p0)
REVERT: C  449 GLU cc_start: 0.7360 (pt0) cc_final: 0.6974 (pt0)
REVERT: C  458 ASP cc_start: 0.8619 (t70) cc_final: 0.8262 (t0)
REVERT: D   72 MET cc_start: 0.8489 (mmm) cc_final: 0.8238 (mmp)
REVERT: D  217 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7628 (mt-10)
REVERT: D  232 HIS cc_start: 0.5814 (m90) cc_final: 0.5399 (m90)
REVERT: D  388 VAL cc_start: 0.9117 (t) cc_final: 0.8799 (t)
REVERT: D  415 PHE cc_start: 0.7959 (t80) cc_final: 0.7351 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 462
  average time/residue: 0.1081
  time to fit residues: 78.8675
Evaluate side-chains
  364 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 152 optimal weight:    9.9990
   chunk 149 optimal weight:    7.9990
   chunk 119 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 159 optimal weight:    8.9990
   chunk 151 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 144 HIS
** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 324 HIS
B 228 GLN
C 161 HIS
C 406 GLN
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.171981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.135461 restraints weight = 20797.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.136522 restraints weight = 17828.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.136874 restraints weight = 14911.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.137857 restraints weight = 12541.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.138054 restraints weight = 10637.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.6211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  16028  Z= 0.202
  Angle     :  0.652   8.508  21668  Z= 0.350
  Chirality :  0.044   0.169   2452
  Planarity :  0.003   0.024   2668
  Dihedral  :  4.494  24.060   2056
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.27 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  1.27 (0.19), residues: 1872
  helix:  1.64 (0.15), residues: 1156
  sheet:  1.76 (0.33), residues: 224
  loop : -1.59 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 165 
 TYR   0.017   0.002   TYR C 106 
 PHE   0.028   0.002   PHE B 524 
 TRP   0.013   0.001   TRP C 431 
 HIS   0.009   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (16028)
  covalent geometry    : angle       0.65188 (21668)
  hydrogen bonds       : bond        0.04732 ( 1063)
  hydrogen bonds       : angle       4.58630 ( 3141)

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

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

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3744 Ramachandran restraints generated.
    1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 453
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8972 (tmm) cc_final: 0.8735 (tmm)
REVERT: A  232 HIS cc_start: 0.6194 (m90) cc_final: 0.5761 (m90)
REVERT: A  335 MET cc_start: 0.6162 (mmm) cc_final: 0.5679 (mtm)
REVERT: A  391 TYR cc_start: 0.7309 (t80) cc_final: 0.7042 (t80)
REVERT: A  415 PHE cc_start: 0.8189 (t80) cc_final: 0.7405 (t80)
REVERT: A  421 MET cc_start: 0.8112 (mmt) cc_final: 0.7796 (mmt)
REVERT: A  471 SER cc_start: 0.9069 (m) cc_final: 0.8837 (t)
REVERT: A  524 PHE cc_start: 0.7294 (t80) cc_final: 0.7013 (t80)
REVERT: B   72 MET cc_start: 0.8511 (mmm) cc_final: 0.8209 (mmp)
REVERT: B  156 MET cc_start: 0.9070 (tmm) cc_final: 0.8843 (tmm)
REVERT: B  232 HIS cc_start: 0.6060 (m90) cc_final: 0.5622 (m90)
REVERT: B  335 MET cc_start: 0.6070 (mmm) cc_final: 0.5754 (mtm)
REVERT: B  361 GLU cc_start: 0.7507 (tp30) cc_final: 0.7205 (tp30)
REVERT: B  415 PHE cc_start: 0.8326 (t80) cc_final: 0.7466 (t80)
REVERT: B  458 ASP cc_start: 0.8578 (t70) cc_final: 0.8262 (t70)
REVERT: C   52 LYS cc_start: 0.8040 (mttt) cc_final: 0.7817 (mttm)
REVERT: C   72 MET cc_start: 0.8548 (mmm) cc_final: 0.8283 (tpp)
REVERT: C  110 MET cc_start: 0.5660 (ttm) cc_final: 0.5419 (ttm)
REVERT: C  232 HIS cc_start: 0.5801 (m90) cc_final: 0.5572 (m90)
REVERT: C  382 MET cc_start: 0.6780 (tmm) cc_final: 0.6557 (tpt)
REVERT: C  415 PHE cc_start: 0.8217 (t80) cc_final: 0.7428 (t80)
REVERT: C  458 ASP cc_start: 0.8657 (t70) cc_final: 0.8370 (t0)
REVERT: D   72 MET cc_start: 0.8481 (mmm) cc_final: 0.8249 (mmp)
REVERT: D  217 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7643 (mt-10)
REVERT: D  232 HIS cc_start: 0.5893 (m90) cc_final: 0.5609 (m90)
REVERT: D  415 PHE cc_start: 0.8094 (t80) cc_final: 0.7510 (t80)
REVERT: D  421 MET cc_start: 0.8340 (mmt) cc_final: 0.8113 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 453
  average time/residue: 0.1063
  time to fit residues: 76.6941
Evaluate side-chains
  351 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 351
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 188
   random chunks:
   chunk 183 optimal weight:    0.7980
   chunk 181 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 72 optimal weight:    3.9990
   chunk 157 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 148 optimal weight:    0.4980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 219 GLN
A 324 HIS
** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 456 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.175876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.140499 restraints weight = 20587.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140944 restraints weight = 13035.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.140880 restraints weight = 11746.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.141211 restraints weight = 10770.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.141435 restraints weight = 10195.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.6374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  16028  Z= 0.143
  Angle     :  0.610  10.882  21668  Z= 0.323
  Chirality :  0.041   0.177   2452
  Planarity :  0.003   0.027   2668
  Dihedral  :  4.456  24.260   2056
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  3.21 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.19), residues: 1872
  helix:  1.73 (0.15), residues: 1148
  sheet:  1.81 (0.33), residues: 224
  loop : -1.75 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 165 
 TYR   0.019   0.001   TYR A 284 
 PHE   0.024   0.002   PHE D 524 
 TRP   0.017   0.001   TRP B 341 
 HIS   0.013   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (16028)
  covalent geometry    : angle       0.60966 (21668)
  hydrogen bonds       : bond        0.04403 ( 1063)
  hydrogen bonds       : angle       4.47943 ( 3141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2556.52 seconds
wall clock time: 45 minutes 15.00 seconds (2715.00 seconds total)