Starting phenix.real_space_refine
on Thu Jul 31 11:05:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vyf_21458/07_2025/6vyf_21458.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      92      5.16       5
     C    8656      2.51       5
     N    2312      2.21       5
     O    2564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13624
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3406
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 14, 'TRANS': 417}
          Chain breaks: 3
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 7.10, per 1000 atoms: 0.52
  Number of scatterers: 13624
  At special positions: 0
  Unit cell: (126.145, 100.248, 117.791, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      92     16.00
     O    2564      8.00
     N    2312      7.00
     C    8656      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.28
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3248

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 12 sheets defined
      47.5% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 166
      removed outlier: 4.279A  pdb=" N   ALA A 157 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
      removed outlier: 4.863A  pdb=" N   GLU A 158 " --> pdb=" O   ASP A 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU A 166 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   PHE A 226 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 227 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR A 245 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
    Processing helix  chain 'A' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS A 312 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE A 325 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 342
    Processing helix  chain 'A' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP A 351 " --> pdb=" O   GLU A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY A 361 " --> pdb=" O   ASN A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 383
      removed outlier: 3.788A  pdb=" N   LYS A 380 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP A 381 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER A 401 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE A 414 " --> pdb=" O   ALA A 410 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A 416 " --> pdb=" O   ALA A 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
      removed outlier: 4.035A  pdb=" N   GLU A 425 " --> pdb=" O   LYS A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 456
      removed outlier: 3.537A  pdb=" N   VAL A 454 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 166
      removed outlier: 4.278A  pdb=" N   ALA B 157 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU B 158 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU B 166 " --> pdb=" O   TYR B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE B 226 " --> pdb=" O   MET B 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR B 245 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 303 through 312
      removed outlier: 3.722A  pdb=" N   TRP B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS B 312 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE B 325 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 342
    Processing helix  chain 'B' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP B 351 " --> pdb=" O   GLU B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY B 361 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
      removed outlier: 3.788A  pdb=" N   LYS B 380 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP B 381 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER B 401 " --> pdb=" O   LYS B 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE B 414 " --> pdb=" O   ALA B 410 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA B 416 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 426
      removed outlier: 4.035A  pdb=" N   GLU B 425 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 456
      removed outlier: 3.538A  pdb=" N   VAL B 454 " --> pdb=" O   GLU B 450 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU B 456 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 461
      No H-bonds generated for 'chain 'B' and resid 459 through 461'
    Processing helix  chain 'B' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA B 476 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.563A  pdb=" N   ASN C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 166
      removed outlier: 4.279A  pdb=" N   ALA C 157 " --> pdb=" O   PHE C 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU C 158 " --> pdb=" O   ASP C 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU C 166 " --> pdb=" O   TYR C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 219 through 229
      removed outlier: 3.885A  pdb=" N   ALA C 225 " --> pdb=" O   LEU C 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE C 226 " --> pdb=" O   MET C 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL C 227 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR C 245 " --> pdb=" O   ASP C 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 296
    Processing helix  chain 'C' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP C 311 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS C 312 " --> pdb=" O   VAL C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.768A  pdb=" N   ILE C 325 " --> pdb=" O   PHE C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 329 through 342
    Processing helix  chain 'C' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP C 351 " --> pdb=" O   GLU C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY C 361 " --> pdb=" O   ASN C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 383
      removed outlier: 3.787A  pdb=" N   LYS C 380 " --> pdb=" O   ARG C 376 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASP C 381 " --> pdb=" O   LYS C 377 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA C 382 " --> pdb=" O   VAL C 378 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER C 401 " --> pdb=" O   LYS C 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA C 416 " --> pdb=" O   ALA C 412 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ILE C 417 " --> pdb=" O   ALA C 413 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 426
      removed outlier: 4.036A  pdb=" N   GLU C 425 " --> pdb=" O   LYS C 422 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 456
      removed outlier: 3.537A  pdb=" N   VAL C 454 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU C 456 " --> pdb=" O   LEU C 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 461
      No H-bonds generated for 'chain 'C' and resid 459 through 461'
    Processing helix  chain 'C' and resid 470 through 486
      removed outlier: 4.601A  pdb=" N   ALA C 476 " --> pdb=" O   SER C 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER C 484 " --> pdb=" O   ALA C 480 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.562A  pdb=" N   ASN D  38 " --> pdb=" O   ASN D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 68
      removed outlier: 3.885A  pdb=" N   GLU D  49 " --> pdb=" O   SER D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 153 through 166
      removed outlier: 4.278A  pdb=" N   ALA D 157 " --> pdb=" O   PHE D 153 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   GLU D 158 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLU D 166 " --> pdb=" O   TYR D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 219 through 229
      removed outlier: 3.884A  pdb=" N   ALA D 225 " --> pdb=" O   LEU D 221 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE D 226 " --> pdb=" O   MET D 222 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL D 227 " --> pdb=" O   ASN D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 252
      removed outlier: 3.635A  pdb=" N   THR D 245 " --> pdb=" O   ASP D 241 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 296
    Processing helix  chain 'D' and resid 303 through 312
      removed outlier: 3.723A  pdb=" N   TRP D 311 " --> pdb=" O   LEU D 307 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   HIS D 312 " --> pdb=" O   VAL D 308 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.769A  pdb=" N   ILE D 325 " --> pdb=" O   PHE D 321 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 342
    Processing helix  chain 'D' and resid 348 through 352
      removed outlier: 3.617A  pdb=" N   TRP D 351 " --> pdb=" O   GLU D 348 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 357 through 366
      removed outlier: 3.647A  pdb=" N   GLY D 361 " --> pdb=" O   ASN D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 376 through 383
      removed outlier: 3.787A  pdb=" N   LYS D 380 " --> pdb=" O   ARG D 376 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASP D 381 " --> pdb=" O   LYS D 377 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA D 382 " --> pdb=" O   VAL D 378 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 388 through 421
      removed outlier: 3.533A  pdb=" N   SER D 401 " --> pdb=" O   LYS D 397 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE D 414 " --> pdb=" O   ALA D 410 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA D 416 " --> pdb=" O   ALA D 412 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE D 417 " --> pdb=" O   ALA D 413 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 422 through 426
      removed outlier: 4.036A  pdb=" N   GLU D 425 " --> pdb=" O   LYS D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 444 through 456
      removed outlier: 3.538A  pdb=" N   VAL D 454 " --> pdb=" O   GLU D 450 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU D 456 " --> pdb=" O   LEU D 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 459 through 461
      No H-bonds generated for 'chain 'D' and resid 459 through 461'
    Processing helix  chain 'D' and resid 470 through 486
      removed outlier: 4.600A  pdb=" N   ALA D 476 " --> pdb=" O   SER D 472 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER D 484 " --> pdb=" O   ALA D 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY A 272 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR A 261 " --> pdb=" O   TYR A 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS A 260 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY A 432 " --> pdb=" O   CYS A 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE A 262 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASP A 434 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ILE A 264 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 101
    Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 178
    Processing sheet with id=AA4, first strand: chain 'B' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY B 272 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   TYR B 261 " --> pdb=" O   TYR B 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS B 260 " --> pdb=" O   SER B 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY B 432 " --> pdb=" O   CYS B 260 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE B 262 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASP B 434 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ILE B 264 " --> pdb=" O   ASP B 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE B 429 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 101
    Processing sheet with id=AA6, first strand: chain 'B' and resid 177 through 178
    Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 83
      removed outlier: 3.967A  pdb=" N   GLY C 272 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   TYR C 261 " --> pdb=" O   TYR C 275 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   CYS C 260 " --> pdb=" O   SER C 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY C 432 " --> pdb=" O   CYS C 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE C 262 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
      removed outlier: 7.776A  pdb=" N   ASP C 434 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ILE C 264 " --> pdb=" O   ASP C 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE C 429 " --> pdb=" O   ILE C 464 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 101
    Processing sheet with id=AA9, first strand: chain 'C' and resid 177 through 178
    Processing sheet with id=AB1, first strand: chain 'D' and resid 82 through 83
      removed outlier: 3.968A  pdb=" N   GLY D 272 " --> pdb=" O   ILE D 291 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   TYR D 261 " --> pdb=" O   TYR D 275 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   CYS D 260 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   GLY D 432 " --> pdb=" O   CYS D 260 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ILE D 262 " --> pdb=" O   GLY D 432 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASP D 434 " --> pdb=" O   ILE D 262 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   ILE D 264 " --> pdb=" O   ASP D 434 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   PHE D 429 " --> pdb=" O   ILE D 464 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 101
    Processing sheet with id=AB3, first strand: chain 'D' and resid 177 through 178

    536 hydrogen bonds defined for protein.
    1536 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: 3.76

  Time building geometry restraints manager: 3.87 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: 4424
        1.34 -     1.46: 3140
        1.46 -     1.58: 6204
        1.58 -     1.70: 0
        1.70 -     1.82: 128
  Bond restraints: 13896
  Sorted by residual:
  bond pdb=" C   HIS A  68 "
       pdb=" N   PRO A  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.321  0.012 8.40e-03 1.42e+04 2.11e+00
  bond pdb=" C   HIS C  68 "
       pdb=" N   PRO C  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 8.40e-03 1.42e+04 1.93e+00
  bond pdb=" C   HIS B  68 "
       pdb=" N   PRO B  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.012 8.40e-03 1.42e+04 1.90e+00
  bond pdb=" C   HIS D  68 "
       pdb=" N   PRO D  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.322  0.011 8.40e-03 1.42e+04 1.86e+00
  bond pdb=" CA  GLN B 319 "
       pdb=" C   GLN B 319 "
    ideal  model  delta    sigma   weight residual
    1.530  1.517  0.013 1.17e-02 7.31e+03 1.29e+00
  ... (remaining 13891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 18424
        2.10 -     4.20: 296
        4.20 -     6.30: 20
        6.30 -     8.40: 0
        8.40 -    10.50: 4
  Bond angle restraints: 18744
  Sorted by residual:
  angle pdb=" CB  MET B 222 "
        pdb=" CG  MET B 222 "
        pdb=" SD  MET B 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.20  -10.50 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET C 222 "
        pdb=" CG  MET C 222 "
        pdb=" SD  MET C 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.17  -10.47 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET A 222 "
        pdb=" CG  MET A 222 "
        pdb=" SD  MET A 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.16  -10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" CB  MET D 222 "
        pdb=" CG  MET D 222 "
        pdb=" SD  MET D 222 "
      ideal   model   delta    sigma   weight residual
     112.70  123.16  -10.46 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   ASN C 315 "
        pdb=" CA  ASN C 315 "
        pdb=" C   ASN C 315 "
      ideal   model   delta    sigma   weight residual
     110.61  106.52    4.09 1.25e+00 6.40e-01 1.07e+01
  ... (remaining 18739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.77: 7116
       13.77 -    27.53: 900
       27.53 -    41.30: 288
       41.30 -    55.06: 52
       55.06 -    68.83: 20
  Dihedral angle restraints: 8376
    sinusoidal: 3352
      harmonic: 5024
  Sorted by residual:
  dihedral pdb=" CA  PHE B 108 "
           pdb=" C   PHE B 108 "
           pdb=" N   ARG B 109 "
           pdb=" CA  ARG B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.55  -33.45     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  PHE C 108 "
           pdb=" C   PHE C 108 "
           pdb=" N   ARG C 109 "
           pdb=" CA  ARG C 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.55  -33.45     0      5.00e+00 4.00e-02 4.47e+01
  dihedral pdb=" CA  PHE A 108 "
           pdb=" C   PHE A 108 "
           pdb=" N   ARG A 109 "
           pdb=" CA  ARG A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.58  -33.42     0      5.00e+00 4.00e-02 4.47e+01
  ... (remaining 8373 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1282
       0.035 -    0.070: 563
       0.070 -    0.105: 144
       0.105 -    0.141: 67
       0.141 -    0.176: 4
  Chirality restraints: 2060
  Sorted by residual:
  chirality pdb=" CA  ILE B 291 "
            pdb=" N   ILE B 291 "
            pdb=" C   ILE B 291 "
            pdb=" CB  ILE B 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.73e-01
  chirality pdb=" CA  ILE C 291 "
            pdb=" N   ILE C 291 "
            pdb=" C   ILE C 291 "
            pdb=" CB  ILE C 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.38e-01
  chirality pdb=" CA  ILE D 291 "
            pdb=" N   ILE D 291 "
            pdb=" C   ILE D 291 "
            pdb=" CB  ILE D 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 2057 not shown)

  Planarity restraints: 2396
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 184 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO C 185 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 185 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 185 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 184 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.48e+00
        pdb=" N   PRO A 185 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 184 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO D 185 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 185 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 185 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2393 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 2386
        2.76 -     3.29: 12880
        3.29 -     3.83: 20541
        3.83 -     4.36: 25628
        4.36 -     4.90: 43787
  Nonbonded interactions: 105222
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 322 "
            pdb=" OG  SER A 326 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLU C 322 "
            pdb=" OG  SER C 326 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLU D 322 "
            pdb=" OG  SER D 326 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   GLU B 322 "
            pdb=" OG  SER B 326 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   PRO B  74 "
            pdb=" ND1 HIS B  75 "
     model   vdw
     2.226 3.120
  ... (remaining 105217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.960
  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:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.370
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
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      :  0.005   0.033  13896  Z= 0.243
  Angle     :  0.678  10.495  18744  Z= 0.404
  Chirality :  0.044   0.176   2060
  Planarity :  0.004   0.040   2396
  Dihedral  : 13.956  68.828   5128
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.73 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  7.46 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.18), residues: 1696
  helix: -2.08 (0.16), residues: 728
  sheet: -0.89 (0.33), residues: 228
  loop : -3.04 (0.19), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.006   0.002   HIS A  75 
 PHE   0.016   0.001   PHE B 108 
 TYR   0.016   0.002   TYR D 162 
 ARG   0.002   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20910 (  536)
  hydrogen bonds       : angle       7.63680 ( 1536)
  covalent geometry    : bond        0.00549 (13896)
  covalent geometry    : angle       0.67764 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 193
  time to evaluate  : 1.645 
Fit side-chains
REVERT: A  124 ASP cc_start: 0.7549 (p0) cc_final: 0.7334 (p0)
REVERT: A  180 PHE cc_start: 0.8068 (t80) cc_final: 0.7790 (t80)
REVERT: A  222 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7177 (tpp)
REVERT: A  318 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7821 (mtp85)
REVERT: B   25 ILE cc_start: 0.7692 (mm) cc_final: 0.7469 (mm)
REVERT: B  180 PHE cc_start: 0.8103 (t80) cc_final: 0.7757 (t80)
REVERT: B  222 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (tpp)
REVERT: B  310 ASP cc_start: 0.8513 (t70) cc_final: 0.8177 (t0)
REVERT: C  180 PHE cc_start: 0.8109 (t80) cc_final: 0.7861 (t80)
REVERT: C  222 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7189 (tpp)
REVERT: D  180 PHE cc_start: 0.8111 (t80) cc_final: 0.7777 (t80)
REVERT: D  222 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7182 (tpp)
REVERT: D  318 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7780 (mtp85)
  outliers start: 4
  outliers final: 0
  residues processed: 193
  average time/residue: 0.3137
  time to fit residues: 83.6285
Evaluate side-chains
  143 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 MET
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain C residue  222 MET
Chi-restraints excluded: chain D residue  222 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    9.9990
   chunk 130 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 134 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 81 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 156 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 366 ASN
A 449 GLN
A 485 GLN
B 340 ASN
B 366 ASN
B 485 GLN
C 366 ASN
C 449 GLN
C 485 GLN
D 340 ASN
D 366 ASN
D 449 GLN
D 485 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.110065 restraints weight = 18992.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.00
r_work: 0.3100 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020  13896  Z= 0.136
  Angle     :  0.528   6.203  18744  Z= 0.288
  Chirality :  0.043   0.149   2060
  Planarity :  0.004   0.036   2396
  Dihedral  :  5.604  46.815   1864
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 12.30 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.19), residues: 1696
  helix: -0.38 (0.20), residues: 728
  sheet: -0.48 (0.34), residues: 228
  loop : -2.85 (0.20), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.006   0.002   HIS C  75 
 PHE   0.015   0.001   PHE B 108 
 TYR   0.012   0.001   TYR B 162 
 ARG   0.002   0.000   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05460 (  536)
  hydrogen bonds       : angle       4.55085 ( 1536)
  covalent geometry    : bond        0.00312 (13896)
  covalent geometry    : angle       0.52803 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 1.663 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8215 (t80) cc_final: 0.7907 (t80)
REVERT: B   25 ILE cc_start: 0.7923 (mm) cc_final: 0.7637 (mm)
REVERT: B  180 PHE cc_start: 0.8304 (t80) cc_final: 0.7885 (t80)
REVERT: B  221 LEU cc_start: 0.7208 (mt) cc_final: 0.6913 (mt)
REVERT: C  180 PHE cc_start: 0.8246 (t80) cc_final: 0.7941 (t80)
REVERT: D  180 PHE cc_start: 0.8270 (t80) cc_final: 0.7883 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 171
  average time/residue: 0.2926
  time to fit residues: 70.7009
Evaluate side-chains
  156 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 104 optimal weight:    9.9990
   chunk 168 optimal weight:    4.9990
   chunk 161 optimal weight:    7.9990
   chunk 165 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0670
   chunk 77 optimal weight:    0.8980
   chunk 123 optimal weight:    6.9990
   chunk 105 optimal weight:   10.0000
   chunk 148 optimal weight:    3.9990
   overall best weight:    3.1924

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

Flipped N/Q/H residues before XYZ refinement:
A 449 GLN
C 290 ASN
C 449 GLN
D 449 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.148746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.108636 restraints weight = 19449.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.97
r_work: 0.3020 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  13896  Z= 0.184
  Angle     :  0.549   5.854  18744  Z= 0.297
  Chirality :  0.044   0.156   2060
  Planarity :  0.003   0.032   2396
  Dihedral  :  5.171  31.527   1852
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.37 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.20), residues: 1696
  helix: -0.01 (0.20), residues: 748
  sheet: -0.35 (0.34), residues: 228
  loop : -2.69 (0.20), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.010   0.002   HIS C  75 
 PHE   0.015   0.001   PHE B 108 
 TYR   0.013   0.002   TYR C 162 
 ARG   0.002   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05840 (  536)
  hydrogen bonds       : angle       4.42231 ( 1536)
  covalent geometry    : bond        0.00443 (13896)
  covalent geometry    : angle       0.54921 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 150
  time to evaluate  : 1.865 
Fit side-chains
REVERT: A   75 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7418 (p-80)
REVERT: A  180 PHE cc_start: 0.8218 (t80) cc_final: 0.7837 (t80)
REVERT: B   25 ILE cc_start: 0.7819 (mm) cc_final: 0.7524 (mm)
REVERT: B   75 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7258 (p-80)
REVERT: B  180 PHE cc_start: 0.8326 (t80) cc_final: 0.7886 (t80)
REVERT: B  221 LEU cc_start: 0.7189 (mt) cc_final: 0.6944 (mt)
REVERT: B  318 ARG cc_start: 0.8547 (mmm-85) cc_final: 0.8283 (mtp85)
REVERT: C   75 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7350 (p-80)
REVERT: C  109 ARG cc_start: 0.7363 (ptt90) cc_final: 0.6839 (ptt90)
REVERT: C  180 PHE cc_start: 0.8233 (t80) cc_final: 0.7864 (t80)
REVERT: D   75 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7370 (p-80)
REVERT: D  180 PHE cc_start: 0.8227 (t80) cc_final: 0.7851 (t80)
  outliers start: 40
  outliers final: 29
  residues processed: 174
  average time/residue: 0.3217
  time to fit residues: 81.3712
Evaluate side-chains
  172 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   75 HIS
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  434 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 48 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0040
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 53 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    1.2794

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

Flipped N/Q/H residues before XYZ refinement:
C 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.152160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.113591 restraints weight = 19251.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.07
r_work: 0.3074 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13896  Z= 0.107
  Angle     :  0.475   5.439  18744  Z= 0.260
  Chirality :  0.042   0.170   2060
  Planarity :  0.003   0.029   2396
  Dihedral  :  4.697  27.526   1852
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 15.26 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.20), residues: 1696
  helix:  0.59 (0.20), residues: 728
  sheet: -0.26 (0.34), residues: 228
  loop : -2.64 (0.19), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 311 
 HIS   0.008   0.002   HIS C  75 
 PHE   0.014   0.001   PHE B 108 
 TYR   0.012   0.001   TYR B 251 
 ARG   0.005   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04466 (  536)
  hydrogen bonds       : angle       4.02347 ( 1536)
  covalent geometry    : bond        0.00240 (13896)
  covalent geometry    : angle       0.47465 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.559 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8185 (t80) cc_final: 0.7864 (t80)
REVERT: B   25 ILE cc_start: 0.7893 (mm) cc_final: 0.7593 (mm)
REVERT: B   75 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7378 (p-80)
REVERT: B  180 PHE cc_start: 0.8296 (t80) cc_final: 0.7883 (t80)
REVERT: B  221 LEU cc_start: 0.7295 (mt) cc_final: 0.7067 (mt)
REVERT: B  338 MET cc_start: 0.9203 (mmm) cc_final: 0.8745 (mmp)
REVERT: B  434 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8019 (t0)
REVERT: C   75 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7442 (p-80)
REVERT: C  109 ARG cc_start: 0.7336 (ptt90) cc_final: 0.6751 (ptt90)
REVERT: C  180 PHE cc_start: 0.8248 (t80) cc_final: 0.7910 (t80)
REVERT: D  180 PHE cc_start: 0.8239 (t80) cc_final: 0.7890 (t80)
  outliers start: 37
  outliers final: 22
  residues processed: 173
  average time/residue: 0.3449
  time to fit residues: 85.8474
Evaluate side-chains
  162 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 2.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  299 ASP
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 137 optimal weight:    9.9990
   chunk 121 optimal weight:    7.9990
   chunk 73 optimal weight:    0.8980
   chunk 115 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 145 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
D 449 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.150096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110120 restraints weight = 19146.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.96
r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023  13896  Z= 0.155
  Angle     :  0.514   5.456  18744  Z= 0.279
  Chirality :  0.043   0.180   2060
  Planarity :  0.003   0.029   2396
  Dihedral  :  4.856  28.273   1852
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.92 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.20), residues: 1696
  helix:  0.55 (0.20), residues: 748
  sheet: -0.22 (0.37), residues: 192
  loop : -2.54 (0.19), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 311 
 HIS   0.013   0.002   HIS D  75 
 PHE   0.014   0.001   PHE B 108 
 TYR   0.012   0.001   TYR D 162 
 ARG   0.004   0.000   ARG C 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05209 (  536)
  hydrogen bonds       : angle       4.11716 ( 1536)
  covalent geometry    : bond        0.00369 (13896)
  covalent geometry    : angle       0.51432 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 138
  time to evaluate  : 1.685 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8203 (t80) cc_final: 0.7892 (t80)
REVERT: B   25 ILE cc_start: 0.7870 (mm) cc_final: 0.7558 (mm)
REVERT: B   75 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7377 (p-80)
REVERT: B  180 PHE cc_start: 0.8316 (t80) cc_final: 0.7879 (t80)
REVERT: B  222 MET cc_start: 0.7284 (tpp) cc_final: 0.7037 (tmm)
REVERT: B  338 MET cc_start: 0.9180 (mmm) cc_final: 0.8756 (mmt)
REVERT: B  434 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.7955 (t0)
REVERT: C   75 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7491 (p-80)
REVERT: C  109 ARG cc_start: 0.7352 (ptt90) cc_final: 0.6818 (ptt90)
REVERT: C  180 PHE cc_start: 0.8237 (t80) cc_final: 0.7874 (t80)
REVERT: C  434 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.7985 (t0)
REVERT: D  180 PHE cc_start: 0.8219 (t80) cc_final: 0.7853 (t80)
REVERT: D  434 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.7987 (t0)
  outliers start: 50
  outliers final: 32
  residues processed: 174
  average time/residue: 0.2606
  time to fit residues: 66.0619
Evaluate side-chains
  173 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  385 MET
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 149 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0050
   chunk 88 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 145 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.151309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.110953 restraints weight = 19442.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.00
r_work: 0.3040 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  13896  Z= 0.137
  Angle     :  0.495   5.247  18744  Z= 0.269
  Chirality :  0.043   0.172   2060
  Planarity :  0.003   0.028   2396
  Dihedral  :  4.760  27.735   1852
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.85 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.20), residues: 1696
  helix:  0.67 (0.20), residues: 748
  sheet: -0.16 (0.38), residues: 192
  loop : -2.49 (0.19), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.012   0.002   HIS A  75 
 PHE   0.014   0.001   PHE B 108 
 TYR   0.012   0.001   TYR C 162 
 ARG   0.002   0.000   ARG A 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04896 (  536)
  hydrogen bonds       : angle       4.03517 ( 1536)
  covalent geometry    : bond        0.00321 (13896)
  covalent geometry    : angle       0.49502 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 139
  time to evaluate  : 2.443 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8178 (t80) cc_final: 0.7854 (t80)
REVERT: B   25 ILE cc_start: 0.7812 (mm) cc_final: 0.7512 (mm)
REVERT: B   75 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7453 (p-80)
REVERT: B  180 PHE cc_start: 0.8294 (t80) cc_final: 0.7832 (t80)
REVERT: B  222 MET cc_start: 0.7287 (tpp) cc_final: 0.7035 (tmm)
REVERT: B  338 MET cc_start: 0.9176 (mmm) cc_final: 0.8947 (mmp)
REVERT: B  434 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.7930 (t70)
REVERT: C   75 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7487 (p-80)
REVERT: C   94 GLU cc_start: 0.7125 (pm20) cc_final: 0.6891 (pm20)
REVERT: C  109 ARG cc_start: 0.7370 (ptt90) cc_final: 0.6805 (ptt90)
REVERT: C  180 PHE cc_start: 0.8204 (t80) cc_final: 0.7896 (t80)
REVERT: C  434 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.7912 (t70)
REVERT: D  180 PHE cc_start: 0.8201 (t80) cc_final: 0.7832 (t80)
REVERT: D  434 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.7895 (t70)
  outliers start: 51
  outliers final: 38
  residues processed: 178
  average time/residue: 0.2913
  time to fit residues: 75.7437
Evaluate side-chains
  176 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   43 THR
Chi-restraints excluded: chain C residue   75 HIS
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   43 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 107 optimal weight:    7.9990
   chunk 84 optimal weight:    0.0070
   chunk 80 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 171 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 142 optimal weight:   10.0000
   overall best weight:    1.1000

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 290 ASN
D 290 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.154414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114988 restraints weight = 19231.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.94
r_work: 0.3088 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13896  Z= 0.099
  Angle     :  0.461   5.137  18744  Z= 0.252
  Chirality :  0.041   0.184   2060
  Planarity :  0.003   0.028   2396
  Dihedral  :  4.456  25.412   1852
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.05 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.20), residues: 1696
  helix:  1.05 (0.20), residues: 728
  sheet:  0.24 (0.38), residues: 184
  loop : -2.56 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 311 
 HIS   0.010   0.002   HIS A  75 
 PHE   0.012   0.001   PHE A 108 
 TYR   0.010   0.001   TYR A 162 
 ARG   0.002   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  536)
  hydrogen bonds       : angle       3.80613 ( 1536)
  covalent geometry    : bond        0.00216 (13896)
  covalent geometry    : angle       0.46071 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 141
  time to evaluate  : 1.684 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8188 (t80) cc_final: 0.7845 (t80)
REVERT: B   25 ILE cc_start: 0.7763 (mm) cc_final: 0.7503 (mm)
REVERT: B  180 PHE cc_start: 0.8226 (t80) cc_final: 0.7806 (t80)
REVERT: B  228 ARG cc_start: 0.3562 (mtp180) cc_final: 0.3289 (mtm180)
REVERT: B  434 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.7691 (t70)
REVERT: C  180 PHE cc_start: 0.8221 (t80) cc_final: 0.7849 (t80)
REVERT: C  434 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.7753 (t70)
REVERT: D  180 PHE cc_start: 0.8213 (t80) cc_final: 0.7815 (t80)
REVERT: D  434 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.7728 (t70)
  outliers start: 58
  outliers final: 34
  residues processed: 181
  average time/residue: 0.2704
  time to fit residues: 71.0124
Evaluate side-chains
  168 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  299 ASP
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 138 optimal weight:    3.9990
   chunk 128 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 135 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0770
   overall best weight:    2.1542

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.151765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111738 restraints weight = 19259.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.98
r_work: 0.3052 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.2065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  13896  Z= 0.135
  Angle     :  0.490   5.166  18744  Z= 0.266
  Chirality :  0.042   0.179   2060
  Planarity :  0.003   0.028   2396
  Dihedral  :  4.583  26.197   1852
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.59 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.20), residues: 1696
  helix:  0.89 (0.20), residues: 748
  sheet:  0.27 (0.38), residues: 184
  loop : -2.48 (0.19), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 311 
 HIS   0.012   0.002   HIS A  75 
 PHE   0.013   0.001   PHE C 108 
 TYR   0.011   0.001   TYR D 162 
 ARG   0.002   0.000   ARG C 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04697 (  536)
  hydrogen bonds       : angle       3.89760 ( 1536)
  covalent geometry    : bond        0.00318 (13896)
  covalent geometry    : angle       0.48994 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 131
  time to evaluate  : 1.474 
Fit side-chains
REVERT: A  180 PHE cc_start: 0.8195 (t80) cc_final: 0.7870 (t80)
REVERT: A  222 MET cc_start: 0.7251 (tpp) cc_final: 0.7007 (tmm)
REVERT: B   25 ILE cc_start: 0.7808 (mm) cc_final: 0.7532 (mm)
REVERT: B  180 PHE cc_start: 0.8254 (t80) cc_final: 0.7795 (t80)
REVERT: B  222 MET cc_start: 0.7508 (mmm) cc_final: 0.7248 (tpt)
REVERT: C  180 PHE cc_start: 0.8204 (t80) cc_final: 0.7895 (t80)
REVERT: C  434 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.7743 (t70)
REVERT: D  180 PHE cc_start: 0.8187 (t80) cc_final: 0.7828 (t80)
  outliers start: 53
  outliers final: 45
  residues processed: 171
  average time/residue: 0.2539
  time to fit residues: 63.3430
Evaluate side-chains
  175 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 129
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  324 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  290 ASN
Chi-restraints excluded: chain B residue  324 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  324 MET
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  324 MET
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 140 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 155 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 164 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 449 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.108998 restraints weight = 19204.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.00
r_work: 0.3007 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  13896  Z= 0.199
  Angle     :  0.555   5.282  18744  Z= 0.300
  Chirality :  0.045   0.181   2060
  Planarity :  0.003   0.029   2396
  Dihedral  :  4.962  28.792   1852
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.06 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.20), residues: 1696
  helix:  0.66 (0.20), residues: 748
  sheet: -0.05 (0.38), residues: 192
  loop : -2.44 (0.19), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 351 
 HIS   0.015   0.003   HIS A  75 
 PHE   0.015   0.001   PHE B 108 
 TYR   0.013   0.002   TYR A 162 
 ARG   0.002   0.000   ARG C 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05686 (  536)
  hydrogen bonds       : angle       4.13819 ( 1536)
  covalent geometry    : bond        0.00482 (13896)
  covalent geometry    : angle       0.55530 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 131
  time to evaluate  : 1.481 
Fit side-chains
REVERT: A  124 ASP cc_start: 0.7821 (p0) cc_final: 0.7606 (p0)
REVERT: A  180 PHE cc_start: 0.8198 (t80) cc_final: 0.7866 (t80)
REVERT: B   25 ILE cc_start: 0.7770 (mm) cc_final: 0.7472 (mm)
REVERT: B  180 PHE cc_start: 0.8253 (t80) cc_final: 0.7792 (t80)
REVERT: B  318 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8345 (mtp85)
REVERT: C  180 PHE cc_start: 0.8230 (t80) cc_final: 0.7890 (t80)
REVERT: D  180 PHE cc_start: 0.8208 (t80) cc_final: 0.7825 (t80)
REVERT: D  222 MET cc_start: 0.7252 (tpp) cc_final: 0.7036 (tmm)
  outliers start: 49
  outliers final: 45
  residues processed: 170
  average time/residue: 0.2777
  time to fit residues: 68.3364
Evaluate side-chains
  171 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 126
  time to evaluate  : 1.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 56 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    3.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.148294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108075 restraints weight = 19328.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.97
r_work: 0.3004 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  13896  Z= 0.209
  Angle     :  0.564   5.316  18744  Z= 0.305
  Chirality :  0.045   0.189   2060
  Planarity :  0.003   0.028   2396
  Dihedral  :  5.138  30.700   1852
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.93 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.20), residues: 1696
  helix:  0.46 (0.19), residues: 748
  sheet: -0.07 (0.38), residues: 192
  loop : -2.41 (0.20), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 351 
 HIS   0.015   0.003   HIS A  75 
 PHE   0.018   0.002   PHE B 108 
 TYR   0.014   0.002   TYR D 162 
 ARG   0.002   0.000   ARG C 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05795 (  536)
  hydrogen bonds       : angle       4.21009 ( 1536)
  covalent geometry    : bond        0.00507 (13896)
  covalent geometry    : angle       0.56429 (18744)

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

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

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3392 Ramachandran restraints generated.
    1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 127
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A  124 ASP cc_start: 0.7654 (p0) cc_final: 0.7440 (p0)
REVERT: A  180 PHE cc_start: 0.8216 (t80) cc_final: 0.7872 (t80)
REVERT: B   25 ILE cc_start: 0.7775 (mm) cc_final: 0.7470 (mm)
REVERT: B  180 PHE cc_start: 0.8254 (t80) cc_final: 0.7832 (t80)
REVERT: C  180 PHE cc_start: 0.8230 (t80) cc_final: 0.7883 (t80)
REVERT: D  180 PHE cc_start: 0.8228 (t80) cc_final: 0.7882 (t80)
  outliers start: 51
  outliers final: 47
  residues processed: 167
  average time/residue: 0.2517
  time to fit residues: 61.5204
Evaluate side-chains
  173 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 126
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 THR
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue  127 THR
Chi-restraints excluded: chain B residue  190 SER
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  367 ASP
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  162 TYR
Chi-restraints excluded: chain C residue  190 SER
Chi-restraints excluded: chain C residue  213 VAL
Chi-restraints excluded: chain C residue  265 ILE
Chi-restraints excluded: chain C residue  291 ILE
Chi-restraints excluded: chain C residue  309 MET
Chi-restraints excluded: chain C residue  367 ASP
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  434 ASP
Chi-restraints excluded: chain C residue  439 VAL
Chi-restraints excluded: chain D residue   18 THR
Chi-restraints excluded: chain D residue  127 THR
Chi-restraints excluded: chain D residue  162 TYR
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  265 ILE
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  309 MET
Chi-restraints excluded: chain D residue  367 ASP
Chi-restraints excluded: chain D residue  433 VAL
Chi-restraints excluded: chain D residue  434 ASP
Chi-restraints excluded: chain D residue  439 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 84 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 157 optimal weight:    0.8980
   chunk 108 optimal weight:    0.0770
   chunk 129 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 138 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
B 290 ASN
D 290 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.154151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.114369 restraints weight = 19233.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.97
r_work: 0.3099 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13896  Z= 0.094
  Angle     :  0.466   5.255  18744  Z= 0.256
  Chirality :  0.041   0.181   2060
  Planarity :  0.003   0.027   2396
  Dihedral  :  4.451  26.179   1852
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.67 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.20), residues: 1696
  helix:  1.12 (0.20), residues: 728
  sheet:  0.37 (0.39), residues: 184
  loop : -2.44 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  72 
 HIS   0.010   0.002   HIS A  75 
 PHE   0.012   0.001   PHE B 108 
 TYR   0.010   0.001   TYR D 162 
 ARG   0.003   0.000   ARG B 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  536)
  hydrogen bonds       : angle       3.74383 ( 1536)
  covalent geometry    : bond        0.00196 (13896)
  covalent geometry    : angle       0.46605 (18744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7742.30 seconds
wall clock time: 136 minutes 36.19 seconds (8196.19 seconds total)