Starting phenix.real_space_refine
on Wed Mar  4 19:59:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lz3_30022/03_2026/6lz3_30022.map"
  }
  resolution = 3.2
  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=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      48      5.16       5
     C   10228      2.51       5
     N    2804      2.21       5
     O    2880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15968
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 486, 3939
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 33, 'TRANS': 452}
    Chain: "A"
      Number of atoms: 53
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 53
          Unusual residues: {'FAD': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.35, per 1000 atoms: 0.21
  Number of scatterers: 15968
  At special positions: 0
  Unit cell: (82.758, 124.137, 124.137, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     P       8     15.00
     O    2880      8.00
     N    2804      7.00
     C   10228      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 595.8 milliseconds
  

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 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:
      88 helices and 4 sheets defined
      50.4% alpha, 3.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 24
      removed outlier: 3.656A  pdb=" N   ARG A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 65
      removed outlier: 3.774A  pdb=" N   ILE A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER A  54 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN A  55 " --> pdb=" O   TRP A  51 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASN A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A  62 " --> pdb=" O   ASN A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 92
      removed outlier: 3.817A  pdb=" N   ALA A  83 " --> pdb=" O   ASP A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 121
      removed outlier: 3.945A  pdb=" N   VAL A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG A 109 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 119 " --> pdb=" O   GLU A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 157
      removed outlier: 3.683A  pdb=" N   ASN A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 3.580A  pdb=" N   ALA A 201 " --> pdb=" O   ALA A 198 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG A 202 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 203 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 220
      removed outlier: 3.728A  pdb=" N   ASP A 212 " --> pdb=" O   TRP A 208 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.563A  pdb=" N   ALA A 224 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR A 226 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.611A  pdb=" N   PHE A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 268
      removed outlier: 3.602A  pdb=" N   LEU A 264 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A 265 " --> pdb=" O   MET A 261 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.905A  pdb=" N   CYS A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 297
      removed outlier: 3.654A  pdb=" N   SER A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 296 " --> pdb=" O   ARG A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 328
      removed outlier: 3.664A  pdb=" N   PHE A 322 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 346
      removed outlier: 3.897A  pdb=" N   TRP A 343 " --> pdb=" O   MET A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 363
      removed outlier: 3.634A  pdb=" N   VAL A 355 " --> pdb=" O   ARG A 351 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 378
      removed outlier: 3.751A  pdb=" N   GLY A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 395
    Processing helix  chain 'A' and resid 423 through 428
      removed outlier: 3.680A  pdb=" N   TRP A 427 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 432
      removed outlier: 3.564A  pdb=" N   ALA A 432 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 429 through 432'
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 446 through 452
    Processing helix  chain 'A' and resid 467 through 480
      removed outlier: 3.857A  pdb=" N   GLY A 473 " --> pdb=" O   ASP A 469 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   GLN A 476 " --> pdb=" O   LYS A 472 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A 480 " --> pdb=" O   GLN A 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 24
      removed outlier: 3.656A  pdb=" N   ARG B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 65
      removed outlier: 3.774A  pdb=" N   ILE B  53 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER B  54 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN B  55 " --> pdb=" O   TRP B  51 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASN B  58 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B  62 " --> pdb=" O   ASN B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 92
      removed outlier: 3.817A  pdb=" N   ALA B  83 " --> pdb=" O   ASP B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 121
      removed outlier: 3.945A  pdb=" N   VAL B 108 " --> pdb=" O   PRO B 104 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG B 109 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 119 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 157
      removed outlier: 3.684A  pdb=" N   ASN B 154 " --> pdb=" O   ASP B 150 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 203
      removed outlier: 3.580A  pdb=" N   ALA B 201 " --> pdb=" O   ALA B 198 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ARG B 202 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA B 203 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 220
      removed outlier: 3.729A  pdb=" N   ASP B 212 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 226
      removed outlier: 3.562A  pdb=" N   ALA B 224 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR B 226 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
      removed outlier: 3.612A  pdb=" N   PHE B 247 " --> pdb=" O   PRO B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 268
      removed outlier: 3.602A  pdb=" N   LEU B 264 " --> pdb=" O   ARG B 260 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL B 265 " --> pdb=" O   MET B 261 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN B 268 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 280
      removed outlier: 3.906A  pdb=" N   CYS B 278 " --> pdb=" O   ALA B 274 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   THR B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 297
      removed outlier: 3.654A  pdb=" N   SER B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 288 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 328
      removed outlier: 3.664A  pdb=" N   PHE B 322 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 346
      removed outlier: 3.897A  pdb=" N   TRP B 343 " --> pdb=" O   MET B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 349 through 363
      removed outlier: 3.634A  pdb=" N   VAL B 355 " --> pdb=" O   ARG B 351 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 361 " --> pdb=" O   ALA B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 378
      removed outlier: 3.751A  pdb=" N   GLY B 371 " --> pdb=" O   PRO B 367 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 395
    Processing helix  chain 'B' and resid 423 through 428
      removed outlier: 3.680A  pdb=" N   TRP B 427 " --> pdb=" O   TYR B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 432
      removed outlier: 3.564A  pdb=" N   ALA B 432 " --> pdb=" O   PRO B 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 429 through 432'
    Processing helix  chain 'B' and resid 441 through 445
    Processing helix  chain 'B' and resid 446 through 452
    Processing helix  chain 'B' and resid 467 through 480
      removed outlier: 3.858A  pdb=" N   GLY B 473 " --> pdb=" O   ASP B 469 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   GLN B 476 " --> pdb=" O   LYS B 472 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER B 480 " --> pdb=" O   GLN B 476 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 24
      removed outlier: 3.655A  pdb=" N   ARG C  24 " --> pdb=" O   ALA C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 65
      removed outlier: 3.773A  pdb=" N   ILE C  53 " --> pdb=" O   SER C  49 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER C  54 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN C  55 " --> pdb=" O   TRP C  51 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASN C  58 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA C  62 " --> pdb=" O   ASN C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 92
      removed outlier: 3.817A  pdb=" N   ALA C  83 " --> pdb=" O   ASP C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 121
      removed outlier: 3.945A  pdb=" N   VAL C 108 " --> pdb=" O   PRO C 104 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG C 109 " --> pdb=" O   ILE C 105 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA C 119 " --> pdb=" O   GLU C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 149 through 157
      removed outlier: 3.683A  pdb=" N   ASN C 154 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ARG C 155 " --> pdb=" O   PRO C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 203
      removed outlier: 3.580A  pdb=" N   ALA C 201 " --> pdb=" O   ALA C 198 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG C 202 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA C 203 " --> pdb=" O   LEU C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 220
      removed outlier: 3.729A  pdb=" N   ASP C 212 " --> pdb=" O   TRP C 208 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS C 213 " --> pdb=" O   GLN C 209 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 226
      removed outlier: 3.563A  pdb=" N   ALA C 224 " --> pdb=" O   GLY C 221 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C 226 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 247
      removed outlier: 3.611A  pdb=" N   PHE C 247 " --> pdb=" O   PRO C 243 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 268
      removed outlier: 3.603A  pdb=" N   LEU C 264 " --> pdb=" O   ARG C 260 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL C 265 " --> pdb=" O   MET C 261 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN C 268 " --> pdb=" O   LEU C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 280
      removed outlier: 3.905A  pdb=" N   CYS C 278 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 297
      removed outlier: 3.654A  pdb=" N   SER C 284 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG C 288 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 328
      removed outlier: 3.664A  pdb=" N   PHE C 322 " --> pdb=" O   ASP C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 346
      removed outlier: 3.896A  pdb=" N   TRP C 343 " --> pdb=" O   MET C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 363
      removed outlier: 3.634A  pdb=" N   VAL C 355 " --> pdb=" O   ARG C 351 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL C 361 " --> pdb=" O   ALA C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 378
      removed outlier: 3.751A  pdb=" N   GLY C 371 " --> pdb=" O   PRO C 367 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP C 377 " --> pdb=" O   LYS C 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 395
    Processing helix  chain 'C' and resid 423 through 428
      removed outlier: 3.681A  pdb=" N   TRP C 427 " --> pdb=" O   TYR C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 432
      removed outlier: 3.564A  pdb=" N   ALA C 432 " --> pdb=" O   PRO C 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 429 through 432'
    Processing helix  chain 'C' and resid 441 through 445
    Processing helix  chain 'C' and resid 446 through 452
    Processing helix  chain 'C' and resid 467 through 480
      removed outlier: 3.857A  pdb=" N   GLY C 473 " --> pdb=" O   ASP C 469 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   GLN C 476 " --> pdb=" O   LYS C 472 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER C 480 " --> pdb=" O   GLN C 476 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 19 through 24
      removed outlier: 3.656A  pdb=" N   ARG D  24 " --> pdb=" O   ALA D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 65
      removed outlier: 3.774A  pdb=" N   ILE D  53 " --> pdb=" O   SER D  49 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   SER D  54 " --> pdb=" O   ARG D  50 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN D  55 " --> pdb=" O   TRP D  51 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN D  58 " --> pdb=" O   SER D  54 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA D  62 " --> pdb=" O   ASN D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 92
      removed outlier: 3.816A  pdb=" N   ALA D  83 " --> pdb=" O   ASP D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 121
      removed outlier: 3.945A  pdb=" N   VAL D 108 " --> pdb=" O   PRO D 104 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG D 109 " --> pdb=" O   ILE D 105 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA D 119 " --> pdb=" O   GLU D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 157
      removed outlier: 3.683A  pdb=" N   ASN D 154 " --> pdb=" O   ASP D 150 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG D 155 " --> pdb=" O   PRO D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 203
      removed outlier: 3.580A  pdb=" N   ALA D 201 " --> pdb=" O   ALA D 198 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG D 202 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA D 203 " --> pdb=" O   LEU D 200 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 220
      removed outlier: 3.728A  pdb=" N   ASP D 212 " --> pdb=" O   TRP D 208 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS D 213 " --> pdb=" O   GLN D 209 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 226
      removed outlier: 3.563A  pdb=" N   ALA D 224 " --> pdb=" O   GLY D 221 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR D 226 " --> pdb=" O   LEU D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 241 through 247
      removed outlier: 3.612A  pdb=" N   PHE D 247 " --> pdb=" O   PRO D 243 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 251 through 268
      removed outlier: 3.602A  pdb=" N   LEU D 264 " --> pdb=" O   ARG D 260 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL D 265 " --> pdb=" O   MET D 261 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASN D 268 " --> pdb=" O   LEU D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 280
      removed outlier: 3.906A  pdb=" N   CYS D 278 " --> pdb=" O   ALA D 274 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   THR D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 297
      removed outlier: 3.655A  pdb=" N   SER D 284 " --> pdb=" O   LEU D 280 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG D 288 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   PHE D 296 " --> pdb=" O   ARG D 292 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 328
      removed outlier: 3.664A  pdb=" N   PHE D 322 " --> pdb=" O   ASP D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 332 through 346
      removed outlier: 3.897A  pdb=" N   TRP D 343 " --> pdb=" O   MET D 339 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 349 through 363
      removed outlier: 3.634A  pdb=" N   VAL D 355 " --> pdb=" O   ARG D 351 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL D 361 " --> pdb=" O   ALA D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 367 through 378
      removed outlier: 3.751A  pdb=" N   GLY D 371 " --> pdb=" O   PRO D 367 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ASP D 377 " --> pdb=" O   LYS D 373 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 385 through 395
    Processing helix  chain 'D' and resid 423 through 428
      removed outlier: 3.681A  pdb=" N   TRP D 427 " --> pdb=" O   TYR D 423 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 429 through 432
      removed outlier: 3.563A  pdb=" N   ALA D 432 " --> pdb=" O   PRO D 429 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 429 through 432'
    Processing helix  chain 'D' and resid 441 through 445
    Processing helix  chain 'D' and resid 446 through 452
    Processing helix  chain 'D' and resid 467 through 480
      removed outlier: 3.857A  pdb=" N   GLY D 473 " --> pdb=" O   ASP D 469 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLN D 476 " --> pdb=" O   LYS D 472 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   SER D 480 " --> pdb=" O   GLN D 476 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76
      removed outlier: 3.670A  pdb=" N   VAL A  73 " --> pdb=" O   PRO A  31 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL A   4 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL A  96 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76
      removed outlier: 3.670A  pdb=" N   VAL B  73 " --> pdb=" O   PRO B  31 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL B   4 " --> pdb=" O   TYR B  97 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL B  96 " --> pdb=" O   GLN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 76
      removed outlier: 3.670A  pdb=" N   VAL C  73 " --> pdb=" O   PRO C  31 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL C   4 " --> pdb=" O   TYR C  97 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL C  96 " --> pdb=" O   GLN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 73 through 76
      removed outlier: 3.671A  pdb=" N   VAL D  73 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL D   4 " --> pdb=" O   TYR D  97 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL D  96 " --> pdb=" O   GLN D 125 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1476 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: 1.82

  Time building geometry restraints manager: 1.71 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: 5109
        1.34 -     1.46: 3092
        1.46 -     1.57: 8182
        1.57 -     1.69: 13
        1.69 -     1.81: 84
  Bond restraints: 16480
  Sorted by residual:
  bond pdb=" N   LEU C 310 "
       pdb=" CA  LEU C 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.537 -0.080 1.29e-02 6.01e+03 3.82e+01
  bond pdb=" N   LEU D 310 "
       pdb=" CA  LEU D 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.537 -0.080 1.29e-02 6.01e+03 3.81e+01
  bond pdb=" N   LEU A 310 "
       pdb=" CA  LEU A 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.537 -0.079 1.29e-02 6.01e+03 3.78e+01
  bond pdb=" N   LEU B 310 "
       pdb=" CA  LEU B 310 "
    ideal  model  delta    sigma   weight residual
    1.457  1.537 -0.079 1.29e-02 6.01e+03 3.77e+01
  bond pdb=" CA  HIS B 309 "
       pdb=" C   HIS B 309 "
    ideal  model  delta    sigma   weight residual
    1.522  1.592 -0.070 1.20e-02 6.94e+03 3.40e+01
  ... (remaining 16475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 22064
        3.45 -     6.89: 354
        6.89 -    10.34: 66
       10.34 -    13.79: 12
       13.79 -    17.23: 12
  Bond angle restraints: 22508
  Sorted by residual:
  angle pdb=" C   LEU A 310 "
        pdb=" N   ARG A 311 "
        pdb=" CA  ARG A 311 "
      ideal   model   delta    sigma   weight residual
     121.54  135.16  -13.62 1.91e+00 2.74e-01 5.09e+01
  angle pdb=" C   LEU B 310 "
        pdb=" N   ARG B 311 "
        pdb=" CA  ARG B 311 "
      ideal   model   delta    sigma   weight residual
     121.54  135.10  -13.56 1.91e+00 2.74e-01 5.04e+01
  angle pdb=" C   LEU C 310 "
        pdb=" N   ARG C 311 "
        pdb=" CA  ARG C 311 "
      ideal   model   delta    sigma   weight residual
     121.54  135.09  -13.55 1.91e+00 2.74e-01 5.03e+01
  angle pdb=" C   LEU D 310 "
        pdb=" N   ARG D 311 "
        pdb=" CA  ARG D 311 "
      ideal   model   delta    sigma   weight residual
     121.54  135.06  -13.52 1.91e+00 2.74e-01 5.01e+01
  angle pdb=" N   VAL A 317 "
        pdb=" CA  VAL A 317 "
        pdb=" C   VAL A 317 "
      ideal   model   delta    sigma   weight residual
     111.91  106.15    5.76 8.90e-01 1.26e+00 4.19e+01
  ... (remaining 22503 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.03: 8776
       22.03 -    44.05: 752
       44.05 -    66.08: 192
       66.08 -    88.10: 16
       88.10 -   110.13: 12
  Dihedral angle restraints: 9748
    sinusoidal: 4084
      harmonic: 5664
  Sorted by residual:
  dihedral pdb=" CA  THR C 395 "
           pdb=" C   THR C 395 "
           pdb=" N   GLY C 396 "
           pdb=" CA  GLY C 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.58   44.42     0      5.00e+00 4.00e-02 7.89e+01
  dihedral pdb=" CA  THR A 395 "
           pdb=" C   THR A 395 "
           pdb=" N   GLY A 396 "
           pdb=" CA  GLY A 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.58   44.42     0      5.00e+00 4.00e-02 7.89e+01
  dihedral pdb=" CA  THR D 395 "
           pdb=" C   THR D 395 "
           pdb=" N   GLY D 396 "
           pdb=" CA  GLY D 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.62   44.38     0      5.00e+00 4.00e-02 7.88e+01
  ... (remaining 9745 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 2059
       0.085 -    0.170: 246
       0.170 -    0.256: 27
       0.256 -    0.341: 0
       0.341 -    0.426: 4
  Chirality restraints: 2336
  Sorted by residual:
  chirality pdb=" CG  LEU C 398 "
            pdb=" CB  LEU C 398 "
            pdb=" CD1 LEU C 398 "
            pdb=" CD2 LEU C 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.16   -0.43 2.00e-01 2.50e+01 4.53e+00
  chirality pdb=" CG  LEU B 398 "
            pdb=" CB  LEU B 398 "
            pdb=" CD1 LEU B 398 "
            pdb=" CD2 LEU B 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.17   -0.42 2.00e-01 2.50e+01 4.48e+00
  chirality pdb=" CG  LEU D 398 "
            pdb=" CB  LEU D 398 "
            pdb=" CD1 LEU D 398 "
            pdb=" CD2 LEU D 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.17   -0.42 2.00e-01 2.50e+01 4.47e+00
  ... (remaining 2333 not shown)

  Planarity restraints: 2884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 304 "    0.074 5.00e-02 4.00e+02   1.14e-01 2.06e+01
        pdb=" N   PRO A 305 "   -0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO A 305 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 305 "    0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 304 "   -0.074 5.00e-02 4.00e+02   1.13e-01 2.06e+01
        pdb=" N   PRO C 305 "    0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO C 305 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO C 305 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 304 "   -0.074 5.00e-02 4.00e+02   1.13e-01 2.06e+01
        pdb=" N   PRO B 305 "    0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO B 305 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO B 305 "   -0.060 5.00e-02 4.00e+02
  ... (remaining 2881 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1712
        2.74 -     3.28: 14569
        3.28 -     3.82: 25967
        3.82 -     4.36: 31817
        4.36 -     4.90: 53062
  Nonbonded interactions: 127127
  Sorted by model distance:
  nonbonded pdb=" O   TRP C 391 "
            pdb=" OG1 THR C 395 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   TRP B 391 "
            pdb=" OG1 THR B 395 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   TRP D 391 "
            pdb=" OG1 THR D 395 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   TRP A 391 "
            pdb=" OG1 THR A 395 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   THR C 378 "
            pdb=" OG1 THR C 378 "
     model   vdw
     2.253 3.040
  ... (remaining 127122 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: 0.02
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.010
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
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      :  0.007   0.091  16484  Z= 0.363
  Angle     :  1.201  17.232  22508  Z= 0.653
  Chirality :  0.058   0.426   2336
  Planarity :  0.009   0.114   2884
  Dihedral  : 17.574 110.126   6092
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  8.68 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  :  8.45 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.44 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.45 (0.11), residues: 1936
  helix: -4.57 (0.06), residues: 984
  sheet: -3.76 (0.32), residues: 132
  loop : -3.81 (0.16), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 406 
 TYR   0.029   0.003   TYR C  43 
 PHE   0.028   0.003   PHE D 313 
 TRP   0.052   0.003   TRP B 483 
 HIS   0.005   0.001   HIS C  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00714 (16480)
  covalent geometry    : angle       1.20091 (22508)
  hydrogen bonds       : bond        0.34713 (  508)
  hydrogen bonds       : angle      11.59708 ( 1476)
  Misc. bond           : bond        0.01114 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 262
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5564 (mmt) cc_final: 0.5347 (mmt)
REVERT: B  413 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6587 (tp30)
REVERT: C  113 LEU cc_start: 0.8773 (tp) cc_final: 0.8564 (tp)
REVERT: D    1 MET cc_start: 0.5536 (mmt) cc_final: 0.5266 (mmt)
  outliers start: 64
  outliers final: 12
  residues processed: 310
  average time/residue: 0.1601
  time to fit residues: 69.3565
Evaluate side-chains
  175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  413 GLU
Chi-restraints excluded: chain B residue  475 LEU
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  212 ASP
Chi-restraints excluded: chain D residue  378 THR
Chi-restraints excluded: chain D residue  475 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 154 ASN
A 244 HIS
A 246 HIS
A 263 GLN
B  59 HIS
B 154 ASN
B 244 HIS
B 246 HIS
B 257 HIS
B 263 GLN
B 365 GLN
C  59 HIS
C 154 ASN
C 244 HIS
C 246 HIS
C 257 HIS
C 263 GLN
D  59 HIS
D 154 ASN
D 210 ASN
D 244 HIS
D 246 HIS
D 263 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.160547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.120943 restraints weight = 22156.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 2.45
r_work: 0.3385 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  16484  Z= 0.151
  Angle     :  0.732   9.550  22508  Z= 0.367
  Chirality :  0.044   0.146   2336
  Planarity :  0.007   0.088   2884
  Dihedral  : 11.926 103.414   2372
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 11.90 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  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 are not related in a simple way.
  whole: -4.76 (0.15), residues: 1936
  helix: -3.01 (0.12), residues: 984
  sheet: -3.41 (0.34), residues: 132
  loop : -3.16 (0.19), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 474 
 TYR   0.021   0.002   TYR C  43 
 PHE   0.009   0.001   PHE D 417 
 TRP   0.015   0.001   TRP C 483 
 HIS   0.003   0.001   HIS C  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (16480)
  covalent geometry    : angle       0.73244 (22508)
  hydrogen bonds       : bond        0.06024 (  508)
  hydrogen bonds       : angle       5.51316 ( 1476)
  Misc. bond           : bond        0.00427 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 174
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5793 (mmt) cc_final: 0.5452 (mmt)
REVERT: A  113 LEU cc_start: 0.8990 (tp) cc_final: 0.8540 (mm)
REVERT: B  113 LEU cc_start: 0.8828 (tp) cc_final: 0.8513 (mm)
REVERT: B  474 ARG cc_start: 0.7071 (tpt90) cc_final: 0.6851 (tpt90)
REVERT: C  113 LEU cc_start: 0.8963 (tp) cc_final: 0.8619 (mm)
REVERT: D    1 MET cc_start: 0.5785 (mmt) cc_final: 0.5138 (mmt)
REVERT: D  113 LEU cc_start: 0.8945 (tp) cc_final: 0.8660 (mm)
  outliers start: 41
  outliers final: 24
  residues processed: 204
  average time/residue: 0.1454
  time to fit residues: 42.9088
Evaluate side-chains
  160 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  412 PHE
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  378 THR
Chi-restraints excluded: chain D residue  412 PHE
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 136 optimal weight:    0.1980
   chunk 135 optimal weight:    0.7980
   chunk 190 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 143 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 159 optimal weight:    4.9990
   chunk 64 optimal weight:    0.1980
   chunk 147 optimal weight:    6.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS
B  99 ASN
B 365 GLN
C  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.160123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120080 restraints weight = 22490.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.49
r_work: 0.3376 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083  16484  Z= 0.131
  Angle     :  0.627   7.260  22508  Z= 0.314
  Chirality :  0.042   0.142   2336
  Planarity :  0.005   0.063   2884
  Dihedral  : 10.666  84.350   2356
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 14.01 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.64 (0.16), residues: 1936
  helix: -1.86 (0.14), residues: 1004
  sheet: -3.24 (0.34), residues: 132
  loop : -2.89 (0.19), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 474 
 TYR   0.023   0.001   TYR A  43 
 PHE   0.010   0.001   PHE D 417 
 TRP   0.021   0.001   TRP A 438 
 HIS   0.003   0.000   HIS B 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (16480)
  covalent geometry    : angle       0.62737 (22508)
  hydrogen bonds       : bond        0.04445 (  508)
  hydrogen bonds       : angle       4.71188 ( 1476)
  Misc. bond           : bond        0.00400 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 150
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A  113 LEU cc_start: 0.8992 (tp) cc_final: 0.8590 (mm)
REVERT: A  289 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7436 (tm-30)
REVERT: B  113 LEU cc_start: 0.8904 (tp) cc_final: 0.8544 (mm)
REVERT: B  485 LEU cc_start: -0.2816 (OUTLIER) cc_final: -0.3020 (tp)
REVERT: C   89 ARG cc_start: 0.8063 (tpp-160) cc_final: 0.7815 (mmp80)
REVERT: C  113 LEU cc_start: 0.8954 (tp) cc_final: 0.8644 (mm)
REVERT: D    1 MET cc_start: 0.5786 (mmt) cc_final: 0.5114 (mmt)
REVERT: D  113 LEU cc_start: 0.9015 (tp) cc_final: 0.8736 (mm)
  outliers start: 48
  outliers final: 29
  residues processed: 183
  average time/residue: 0.1242
  time to fit residues: 34.1939
Evaluate side-chains
  166 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   99 ASN
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  412 PHE
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  412 PHE
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 191 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   chunk 175 optimal weight:    4.9990
   chunk 56 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 88 optimal weight:    8.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  99 ASN
D 257 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.155279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114260 restraints weight = 22298.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.49
r_work: 0.3289 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  16484  Z= 0.208
  Angle     :  0.682   7.196  22508  Z= 0.336
  Chirality :  0.045   0.141   2336
  Planarity :  0.005   0.057   2884
  Dihedral  : 10.905  70.177   2353
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.94 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.18), residues: 1936
  helix: -1.40 (0.15), residues: 1024
  sheet: -3.18 (0.36), residues: 132
  loop : -2.69 (0.21), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A   8 
 TYR   0.019   0.002   TYR D  43 
 PHE   0.014   0.002   PHE C 281 
 TRP   0.018   0.002   TRP A   6 
 HIS   0.007   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (16480)
  covalent geometry    : angle       0.68192 (22508)
  hydrogen bonds       : bond        0.04551 (  508)
  hydrogen bonds       : angle       4.65878 ( 1476)
  Misc. bond           : bond        0.00513 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 147
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5678 (mmt) cc_final: 0.5407 (mmt)
REVERT: A  113 LEU cc_start: 0.9078 (tp) cc_final: 0.8619 (mm)
REVERT: A  409 ASN cc_start: 0.6246 (t0) cc_final: 0.5801 (t0)
REVERT: B  113 LEU cc_start: 0.8939 (tp) cc_final: 0.8564 (mm)
REVERT: B  394 ILE cc_start: 0.8195 (tp) cc_final: 0.7727 (tp)
REVERT: B  485 LEU cc_start: -0.2821 (OUTLIER) cc_final: -0.3023 (tp)
REVERT: C   89 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7829 (mmp80)
REVERT: C  113 LEU cc_start: 0.8952 (tp) cc_final: 0.8628 (mm)
REVERT: C  394 ILE cc_start: 0.8124 (tp) cc_final: 0.7681 (tp)
REVERT: D    1 MET cc_start: 0.5868 (mmt) cc_final: 0.5039 (mmt)
REVERT: D   86 GLN cc_start: 0.8552 (tp40) cc_final: 0.8279 (tp40)
REVERT: D  113 LEU cc_start: 0.9007 (tp) cc_final: 0.8680 (mm)
REVERT: D  394 ILE cc_start: 0.8137 (tp) cc_final: 0.7891 (tp)
  outliers start: 54
  outliers final: 42
  residues processed: 181
  average time/residue: 0.1191
  time to fit residues: 33.1298
Evaluate side-chains
  183 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 140
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  378 THR
Chi-restraints excluded: chain C residue  412 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  275 GLU
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  335 VAL
Chi-restraints excluded: chain D residue  412 PHE
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  485 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 154 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 188 optimal weight:    2.9990
   chunk 156 optimal weight:    0.2980
   chunk 152 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  99 ASN
B 365 GLN
C  99 ASN
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.157985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.117577 restraints weight = 22054.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.47
r_work: 0.3338 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  16484  Z= 0.116
  Angle     :  0.575   7.206  22508  Z= 0.288
  Chirality :  0.041   0.124   2336
  Planarity :  0.004   0.053   2884
  Dihedral  : 10.454  74.830   2353
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.85 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.18), residues: 1936
  helix: -0.98 (0.16), residues: 1032
  sheet: -3.06 (0.36), residues: 132
  loop : -2.59 (0.21), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.019   0.001   TYR A  43 
 PHE   0.008   0.001   PHE D 359 
 TRP   0.013   0.001   TRP D   6 
 HIS   0.006   0.001   HIS D 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (16480)
  covalent geometry    : angle       0.57467 (22508)
  hydrogen bonds       : bond        0.03843 (  508)
  hydrogen bonds       : angle       4.32194 ( 1476)
  Misc. bond           : bond        0.00383 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 146
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5579 (mmt) cc_final: 0.5300 (mmt)
REVERT: A  113 LEU cc_start: 0.9042 (tp) cc_final: 0.8607 (mm)
REVERT: A  115 GLU cc_start: 0.8865 (tp30) cc_final: 0.8654 (pt0)
REVERT: A  394 ILE cc_start: 0.7955 (tp) cc_final: 0.7438 (tp)
REVERT: A  409 ASN cc_start: 0.6177 (t0) cc_final: 0.5887 (t0)
REVERT: B  113 LEU cc_start: 0.8891 (tp) cc_final: 0.8526 (mm)
REVERT: C   89 ARG cc_start: 0.8148 (tpp-160) cc_final: 0.7810 (mmp80)
REVERT: C  113 LEU cc_start: 0.8894 (tp) cc_final: 0.8545 (mm)
REVERT: C  394 ILE cc_start: 0.8158 (tp) cc_final: 0.7685 (tp)
REVERT: D    1 MET cc_start: 0.5816 (mmt) cc_final: 0.4986 (mmt)
REVERT: D   86 GLN cc_start: 0.8485 (tp40) cc_final: 0.8179 (tp40)
REVERT: D   89 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7649 (mmp80)
REVERT: D  113 LEU cc_start: 0.8992 (tp) cc_final: 0.8657 (mm)
REVERT: D  394 ILE cc_start: 0.8127 (tp) cc_final: 0.7839 (tp)
  outliers start: 50
  outliers final: 38
  residues processed: 181
  average time/residue: 0.1181
  time to fit residues: 32.6261
Evaluate side-chains
  175 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  412 PHE
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  412 PHE
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  412 PHE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  449 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  412 PHE
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  449 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 172 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0170
   chunk 152 optimal weight:    4.9990
   chunk 181 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9990
   chunk 160 optimal weight:    0.2980
   chunk 59 optimal weight:    5.9990
   chunk 97 optimal weight:    1.9990
   chunk 141 optimal weight:    4.9990
   overall best weight:    0.8022

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 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 = 0.4011 r_free = 0.4011 target = 0.158396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.118085 restraints weight = 21910.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.49
r_work: 0.3345 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  16484  Z= 0.115
  Angle     :  0.556   6.363  22508  Z= 0.278
  Chirality :  0.041   0.134   2336
  Planarity :  0.004   0.054   2884
  Dihedral  :  9.974  70.427   2352
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.33 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.18), residues: 1936
  helix: -0.66 (0.16), residues: 1036
  sheet: -2.84 (0.37), residues: 132
  loop : -2.41 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A   8 
 TYR   0.015   0.001   TYR C  43 
 PHE   0.008   0.001   PHE D 359 
 TRP   0.014   0.001   TRP B 443 
 HIS   0.002   0.001   HIS B 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (16480)
  covalent geometry    : angle       0.55590 (22508)
  hydrogen bonds       : bond        0.03600 (  508)
  hydrogen bonds       : angle       4.13849 ( 1476)
  Misc. bond           : bond        0.00360 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 155
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 LEU cc_start: 0.8946 (tp) cc_final: 0.8478 (mm)
REVERT: A  115 GLU cc_start: 0.8914 (tp30) cc_final: 0.8682 (pt0)
REVERT: A  394 ILE cc_start: 0.8125 (tp) cc_final: 0.7595 (tp)
REVERT: A  409 ASN cc_start: 0.6261 (t0) cc_final: 0.5994 (t0)
REVERT: B  113 LEU cc_start: 0.8875 (tp) cc_final: 0.8516 (mm)
REVERT: B  289 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: B  394 ILE cc_start: 0.8143 (tp) cc_final: 0.7683 (tp)
REVERT: C   86 GLN cc_start: 0.8380 (tp40) cc_final: 0.8013 (tp40)
REVERT: C   89 ARG cc_start: 0.8235 (tpp-160) cc_final: 0.7956 (mmm160)
REVERT: C  113 LEU cc_start: 0.8891 (tp) cc_final: 0.8518 (mm)
REVERT: C  394 ILE cc_start: 0.8244 (tp) cc_final: 0.7802 (tp)
REVERT: D   86 GLN cc_start: 0.8500 (tp40) cc_final: 0.8201 (tp40)
REVERT: D   89 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7659 (mmp80)
REVERT: D  113 LEU cc_start: 0.8974 (tp) cc_final: 0.8544 (mm)
REVERT: D  144 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8269 (mm110)
REVERT: D  394 ILE cc_start: 0.8264 (tp) cc_final: 0.7980 (tp)
  outliers start: 54
  outliers final: 39
  residues processed: 196
  average time/residue: 0.1213
  time to fit residues: 36.2776
Evaluate side-chains
  184 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 145
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  449 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  275 GLU
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  449 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 167 optimal weight:    0.0020
   chunk 110 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 158 optimal weight:    0.9980
   chunk 122 optimal weight:    0.7980
   chunk 162 optimal weight:    6.9990
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 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 = 0.4004 r_free = 0.4004 target = 0.157943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.117501 restraints weight = 21892.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 2.48
r_work: 0.3334 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  16484  Z= 0.122
  Angle     :  0.563   6.552  22508  Z= 0.281
  Chirality :  0.041   0.130   2336
  Planarity :  0.004   0.053   2884
  Dihedral  :  9.870  69.555   2352
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.81 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.19), residues: 1936
  helix: -0.52 (0.16), residues: 1036
  sheet: -2.70 (0.37), residues: 132
  loop : -2.32 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.016   0.001   TYR A  43 
 PHE   0.008   0.001   PHE D 359 
 TRP   0.017   0.001   TRP B 443 
 HIS   0.002   0.001   HIS C 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (16480)
  covalent geometry    : angle       0.56310 (22508)
  hydrogen bonds       : bond        0.03621 (  508)
  hydrogen bonds       : angle       4.11877 ( 1476)
  Misc. bond           : bond        0.00378 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 148
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 LEU cc_start: 0.8974 (tp) cc_final: 0.8517 (mm)
REVERT: A  115 GLU cc_start: 0.8877 (tp30) cc_final: 0.8654 (pt0)
REVERT: A  289 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: A  409 ASN cc_start: 0.6277 (t0) cc_final: 0.6005 (t0)
REVERT: B  113 LEU cc_start: 0.8844 (tp) cc_final: 0.8529 (mm)
REVERT: B  289 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: B  394 ILE cc_start: 0.8224 (tp) cc_final: 0.7838 (tp)
REVERT: C   86 GLN cc_start: 0.8386 (tp40) cc_final: 0.8025 (tp40)
REVERT: C   89 ARG cc_start: 0.8207 (tpp-160) cc_final: 0.7929 (mmm160)
REVERT: C  113 LEU cc_start: 0.8816 (tp) cc_final: 0.8527 (mm)
REVERT: D   86 GLN cc_start: 0.8452 (tp40) cc_final: 0.8190 (tp40)
REVERT: D   89 ARG cc_start: 0.7949 (tpp-160) cc_final: 0.7553 (mmp80)
REVERT: D  113 LEU cc_start: 0.8960 (tp) cc_final: 0.8571 (mm)
  outliers start: 50
  outliers final: 41
  residues processed: 186
  average time/residue: 0.1188
  time to fit residues: 33.7962
Evaluate side-chains
  181 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 140
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  449 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  275 GLU
Chi-restraints excluded: chain D residue  335 VAL
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  449 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 143 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 156 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 160 optimal weight:    0.0470
   chunk 180 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 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 = 0.4020 r_free = 0.4020 target = 0.159155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.119062 restraints weight = 22036.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.49
r_work: 0.3360 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  16484  Z= 0.107
  Angle     :  0.545   7.200  22508  Z= 0.273
  Chirality :  0.041   0.142   2336
  Planarity :  0.004   0.053   2884
  Dihedral  :  9.630  70.288   2352
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.63 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.19), residues: 1936
  helix: -0.33 (0.16), residues: 1032
  sheet: -2.63 (0.37), residues: 132
  loop : -2.23 (0.22), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C   8 
 TYR   0.013   0.001   TYR D 415 
 PHE   0.008   0.001   PHE D 359 
 TRP   0.018   0.001   TRP B 443 
 HIS   0.002   0.000   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (16480)
  covalent geometry    : angle       0.54493 (22508)
  hydrogen bonds       : bond        0.03393 (  508)
  hydrogen bonds       : angle       4.00897 ( 1476)
  Misc. bond           : bond        0.00357 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 148
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: A  409 ASN cc_start: 0.6312 (t0) cc_final: 0.6021 (t0)
REVERT: B   89 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7554 (mmt-90)
REVERT: B  113 LEU cc_start: 0.8773 (tp) cc_final: 0.8461 (mm)
REVERT: B  144 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8259 (mm110)
REVERT: B  289 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: B  426 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7826 (tpt90)
REVERT: C   86 GLN cc_start: 0.8371 (tp40) cc_final: 0.8007 (tp40)
REVERT: C   89 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7868 (mmm160)
REVERT: C  113 LEU cc_start: 0.8872 (tp) cc_final: 0.8501 (mm)
REVERT: C  144 GLN cc_start: 0.8344 (mm110) cc_final: 0.8124 (mm110)
REVERT: C  394 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7965 (tp)
REVERT: D   86 GLN cc_start: 0.8430 (tp40) cc_final: 0.8152 (tp40)
REVERT: D   89 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.7539 (mmp80)
REVERT: D  113 LEU cc_start: 0.8943 (tp) cc_final: 0.8528 (mm)
REVERT: D  394 ILE cc_start: 0.8266 (tp) cc_final: 0.7936 (tp)
  outliers start: 52
  outliers final: 44
  residues processed: 186
  average time/residue: 0.1258
  time to fit residues: 34.9006
Evaluate side-chains
  188 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  394 ILE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  449 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  275 GLU
Chi-restraints excluded: chain D residue  310 LEU
Chi-restraints excluded: chain D residue  335 VAL
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  449 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 110 optimal weight:    3.9990
   chunk 121 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 173 optimal weight:    0.9980
   chunk 79 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 103 optimal weight:    0.5980
   chunk 191 optimal weight:    7.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 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 = 0.3989 r_free = 0.3989 target = 0.156646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.116014 restraints weight = 22031.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.51
r_work: 0.3303 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  16484  Z= 0.160
  Angle     :  0.598   6.797  22508  Z= 0.295
  Chirality :  0.043   0.133   2336
  Planarity :  0.004   0.052   2884
  Dihedral  : 10.031  67.815   2352
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.63 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.19), residues: 1936
  helix: -0.37 (0.16), residues: 1020
  sheet: -2.52 (0.38), residues: 132
  loop : -2.16 (0.22), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   8 
 TYR   0.015   0.002   TYR D  43 
 PHE   0.011   0.001   PHE A 281 
 TRP   0.021   0.001   TRP B 443 
 HIS   0.004   0.001   HIS B 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (16480)
  covalent geometry    : angle       0.59785 (22508)
  hydrogen bonds       : bond        0.03850 (  508)
  hydrogen bonds       : angle       4.17165 ( 1476)
  Misc. bond           : bond        0.00448 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 140
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 LEU cc_start: 0.8865 (tp) cc_final: 0.8613 (mm)
REVERT: A  409 ASN cc_start: 0.6384 (t0) cc_final: 0.6045 (t0)
REVERT: A  479 LEU cc_start: 0.4381 (OUTLIER) cc_final: 0.4148 (tp)
REVERT: B   14 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: B  113 LEU cc_start: 0.8826 (tp) cc_final: 0.8456 (mm)
REVERT: B  144 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8270 (mm110)
REVERT: B  289 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: C   86 GLN cc_start: 0.8424 (tp40) cc_final: 0.8151 (tp40)
REVERT: C   89 ARG cc_start: 0.8222 (tpp-160) cc_final: 0.7829 (mmp80)
REVERT: C  113 LEU cc_start: 0.8820 (tp) cc_final: 0.8425 (mm)
REVERT: C  144 GLN cc_start: 0.8266 (mm110) cc_final: 0.8057 (mm110)
REVERT: C  394 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8122 (tp)
REVERT: D    1 MET cc_start: 0.5797 (mmt) cc_final: 0.5536 (mmt)
REVERT: D   89 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7630 (mmp80)
REVERT: D  113 LEU cc_start: 0.8963 (tp) cc_final: 0.8532 (mm)
REVERT: D  394 ILE cc_start: 0.8443 (tp) cc_final: 0.8188 (tp)
REVERT: D  474 ARG cc_start: 0.6998 (tpt90) cc_final: 0.6758 (tpt90)
  outliers start: 54
  outliers final: 41
  residues processed: 180
  average time/residue: 0.1276
  time to fit residues: 34.6689
Evaluate side-chains
  182 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 139
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  252 VAL
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  394 ILE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  252 VAL
Chi-restraints excluded: chain D residue  335 VAL
Chi-restraints excluded: chain D residue  430 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 62 optimal weight:    9.9990
   chunk 156 optimal weight:    0.0010
   chunk 21 optimal weight:    0.7980
   chunk 157 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0040
   chunk 124 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 ASN
B 365 GLN
** C 297 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 = 0.4025 r_free = 0.4025 target = 0.159411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.120160 restraints weight = 21860.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.47
r_work: 0.3376 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  16484  Z= 0.100
  Angle     :  0.538   6.423  22508  Z= 0.269
  Chirality :  0.040   0.122   2336
  Planarity :  0.004   0.052   2884
  Dihedral  :  9.558  72.251   2352
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.78 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.19), residues: 1936
  helix: -0.06 (0.17), residues: 1008
  sheet: -2.42 (0.37), residues: 132
  loop : -2.15 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  75 
 TYR   0.013   0.001   TYR D 415 
 PHE   0.007   0.001   PHE B 313 
 TRP   0.024   0.001   TRP B 443 
 HIS   0.002   0.000   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (16480)
  covalent geometry    : angle       0.53774 (22508)
  hydrogen bonds       : bond        0.03263 (  508)
  hydrogen bonds       : angle       3.98382 ( 1476)
  Misc. bond           : bond        0.00335 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 TYR cc_start: 0.7304 (m-80) cc_final: 0.6903 (m-10)
REVERT: A   89 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7532 (mmp80)
REVERT: A  113 LEU cc_start: 0.8807 (tp) cc_final: 0.8454 (mm)
REVERT: A  289 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7297 (tm-30)
REVERT: A  394 ILE cc_start: 0.8269 (tp) cc_final: 0.7979 (tp)
REVERT: A  409 ASN cc_start: 0.6298 (t0) cc_final: 0.5981 (t0)
REVERT: B   14 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: B   43 TYR cc_start: 0.7332 (m-80) cc_final: 0.6986 (m-10)
REVERT: B   89 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.7566 (mmt-90)
REVERT: B  113 LEU cc_start: 0.8785 (tp) cc_final: 0.8457 (mm)
REVERT: B  180 MET cc_start: 0.5488 (ttm) cc_final: 0.4894 (tpt)
REVERT: B  289 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: B  394 ILE cc_start: 0.8331 (tp) cc_final: 0.8123 (tp)
REVERT: B  426 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7832 (tpt90)
REVERT: C   89 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7865 (mmm160)
REVERT: C  113 LEU cc_start: 0.8821 (tp) cc_final: 0.8476 (mm)
REVERT: C  394 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (tp)
REVERT: D   86 GLN cc_start: 0.8416 (tp40) cc_final: 0.8145 (tp40)
REVERT: D   89 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.7558 (mmp80)
REVERT: D  113 LEU cc_start: 0.8944 (tp) cc_final: 0.8514 (mm)
REVERT: D  289 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7337 (tm-30)
REVERT: D  394 ILE cc_start: 0.8407 (tp) cc_final: 0.8156 (tp)
  outliers start: 36
  outliers final: 34
  residues processed: 169
  average time/residue: 0.1342
  time to fit residues: 33.4948
Evaluate side-chains
  176 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  181 CYS
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  430 GLU
Chi-restraints excluded: chain B residue  449 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  181 CYS
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  394 ILE
Chi-restraints excluded: chain C residue  428 ILE
Chi-restraints excluded: chain C residue  449 VAL
Chi-restraints excluded: chain C residue  485 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  181 CYS
Chi-restraints excluded: chain D residue  251 SER
Chi-restraints excluded: chain D residue  335 VAL
Chi-restraints excluded: chain D residue  430 GLU
Chi-restraints excluded: chain D residue  449 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   chunk 126 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 169 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 175 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 392 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.159023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.119004 restraints weight = 21795.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.50
r_work: 0.3351 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16484  Z= 0.113
  Angle     :  0.547   6.313  22508  Z= 0.272
  Chirality :  0.041   0.116   2336
  Planarity :  0.004   0.052   2884
  Dihedral  :  9.648  69.723   2352
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.36 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.19), residues: 1936
  helix: -0.04 (0.17), residues: 1008
  sheet: -2.33 (0.38), residues: 132
  loop : -2.12 (0.22), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 474 
 TYR   0.012   0.001   TYR D 415 
 PHE   0.009   0.001   PHE D 359 
 TRP   0.020   0.001   TRP B 443 
 HIS   0.003   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (16480)
  covalent geometry    : angle       0.54667 (22508)
  hydrogen bonds       : bond        0.03374 (  508)
  hydrogen bonds       : angle       3.97458 ( 1476)
  Misc. bond           : bond        0.00360 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3247.01 seconds
wall clock time: 56 minutes 23.45 seconds (3383.45 seconds total)