Starting phenix.real_space_refine
on Thu Sep 18 08:15:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rwk_19549/09_2025/8rwk_19549.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      44      5.16       5
     C    9772      2.51       5
     N    2588      2.21       5
     O    3000      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15416
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 3806
          Classifications: {'peptide': 495}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 473}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 3.21, per 1000 atoms: 0.21
  Number of scatterers: 15416
  At special positions: 0
  Unit cell: (113.3, 115.5, 102.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P      12     15.00
     O    3000      8.00
     N    2588      7.00
     C    9772      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 726.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3608

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 18 sheets defined
      42.2% alpha, 19.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 80 through 97
    Processing helix  chain 'A' and resid 105 through 121
    Processing helix  chain 'A' and resid 122 through 135
    Processing helix  chain 'A' and resid 137 through 156
      removed outlier: 3.589A  pdb=" N   ARG A 142 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLY A 143 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP A 144 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 193 through 207
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 221 through 227
      removed outlier: 3.639A  pdb=" N   LEU A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 247 through 257
      removed outlier: 4.057A  pdb=" N   GLU A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 282
      removed outlier: 3.680A  pdb=" N   ALA A 282 " --> pdb=" O   GLN A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 318
    Processing helix  chain 'A' and resid 319 through 322
    Processing helix  chain 'A' and resid 336 through 349
      removed outlier: 3.875A  pdb=" N   GLU A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 386
    Processing helix  chain 'A' and resid 415 through 419
    Processing helix  chain 'A' and resid 434 through 443
    Processing helix  chain 'A' and resid 457 through 466
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'B' and resid 80 through 97
    Processing helix  chain 'B' and resid 105 through 121
    Processing helix  chain 'B' and resid 122 through 135
    Processing helix  chain 'B' and resid 137 through 156
      removed outlier: 3.589A  pdb=" N   ARG B 142 " --> pdb=" O   ILE B 138 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLY B 143 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP B 144 " --> pdb=" O   SER B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 193 through 207
      Proline residue:  B 204  - end of helix
    Processing helix  chain 'B' and resid 221 through 227
      removed outlier: 3.639A  pdb=" N   LEU B 225 " --> pdb=" O   PRO B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
    Processing helix  chain 'B' and resid 247 through 257
      removed outlier: 4.057A  pdb=" N   GLU B 253 " --> pdb=" O   LYS B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 282
      removed outlier: 3.680A  pdb=" N   ALA B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 318
    Processing helix  chain 'B' and resid 319 through 322
    Processing helix  chain 'B' and resid 336 through 349
      removed outlier: 3.875A  pdb=" N   GLU B 349 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 386
    Processing helix  chain 'B' and resid 415 through 419
    Processing helix  chain 'B' and resid 434 through 443
    Processing helix  chain 'B' and resid 457 through 466
    Processing helix  chain 'B' and resid 500 through 506
    Processing helix  chain 'C' and resid 80 through 97
    Processing helix  chain 'C' and resid 105 through 121
    Processing helix  chain 'C' and resid 122 through 135
    Processing helix  chain 'C' and resid 137 through 156
      removed outlier: 3.590A  pdb=" N   ARG C 142 " --> pdb=" O   ILE C 138 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   GLY C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASP C 144 " --> pdb=" O   SER C 140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'C' and resid 193 through 207
      Proline residue:  C 204  - end of helix
    Processing helix  chain 'C' and resid 221 through 227
      removed outlier: 3.639A  pdb=" N   LEU C 225 " --> pdb=" O   PRO C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 230 through 235
    Processing helix  chain 'C' and resid 247 through 257
      removed outlier: 4.057A  pdb=" N   GLU C 253 " --> pdb=" O   LYS C 249 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 282
      removed outlier: 3.680A  pdb=" N   ALA C 282 " --> pdb=" O   GLN C 278 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 318
    Processing helix  chain 'C' and resid 319 through 322
    Processing helix  chain 'C' and resid 336 through 349
      removed outlier: 3.874A  pdb=" N   GLU C 349 " --> pdb=" O   LYS C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 386
    Processing helix  chain 'C' and resid 415 through 419
    Processing helix  chain 'C' and resid 434 through 443
    Processing helix  chain 'C' and resid 457 through 466
    Processing helix  chain 'C' and resid 500 through 506
    Processing helix  chain 'D' and resid 80 through 97
    Processing helix  chain 'D' and resid 105 through 121
    Processing helix  chain 'D' and resid 122 through 135
    Processing helix  chain 'D' and resid 137 through 156
      removed outlier: 3.589A  pdb=" N   ARG D 142 " --> pdb=" O   ILE D 138 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLY D 143 " --> pdb=" O   SER D 139 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP D 144 " --> pdb=" O   SER D 140 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 193 through 207
      Proline residue:  D 204  - end of helix
    Processing helix  chain 'D' and resid 221 through 227
      removed outlier: 3.639A  pdb=" N   LEU D 225 " --> pdb=" O   PRO D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 235
    Processing helix  chain 'D' and resid 247 through 257
      removed outlier: 4.057A  pdb=" N   GLU D 253 " --> pdb=" O   LYS D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 282
      removed outlier: 3.679A  pdb=" N   ALA D 282 " --> pdb=" O   GLN D 278 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 304 through 318
    Processing helix  chain 'D' and resid 319 through 322
    Processing helix  chain 'D' and resid 336 through 349
      removed outlier: 3.875A  pdb=" N   GLU D 349 " --> pdb=" O   LYS D 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 368 through 386
    Processing helix  chain 'D' and resid 415 through 419
    Processing helix  chain 'D' and resid 434 through 443
    Processing helix  chain 'D' and resid 457 through 466
    Processing helix  chain 'D' and resid 500 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 35
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 65
      removed outlier: 7.179A  pdb=" N   LYS A  60 " --> pdb=" O   TYR A  77 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   TYR A  77 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   PHE A  62 " --> pdb=" O   HIS A  75 " (cutoff:3.500A)
      removed outlier: 4.719A  pdb=" N   HIS A  75 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL A  64 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 391
      removed outlier: 6.392A  pdb=" N   VAL B 407 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   VAL B 330 " --> pdb=" O   THR B 430 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   PHE B 432 " --> pdb=" O   VAL B 330 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   VAL B 332 " --> pdb=" O   PHE B 432 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ASN B 297 " --> pdb=" O   TYR B 331 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLU B 333 " --> pdb=" O   ASN B 297 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   VAL B 299 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA B 451 " --> pdb=" O   TRP B 474 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 175 " --> pdb=" O   ILE A 167 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER D 175 " --> pdb=" O   ILE D 167 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   VAL C 473 " --> pdb=" O   ARG D 514 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   LYS D 516 " --> pdb=" O   VAL C 473 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE C 475 " --> pdb=" O   LYS D 516 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ALA C 451 " --> pdb=" O   TRP C 474 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ASN C 297 " --> pdb=" O   TYR C 331 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLU C 333 " --> pdb=" O   ASN C 297 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   VAL C 299 " --> pdb=" O   GLU C 333 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   VAL C 330 " --> pdb=" O   THR C 430 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   PHE C 432 " --> pdb=" O   VAL C 330 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL C 332 " --> pdb=" O   PHE C 432 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL C 407 " --> pdb=" O   ILE C 390 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 241 through 245
      removed outlier: 6.607A  pdb=" N   CYS A 185 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   LYS A 215 " --> pdb=" O   CYS A 185 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLN A 187 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS A 263 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   THR A 267 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 391
      removed outlier: 6.393A  pdb=" N   VAL A 407 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   VAL A 330 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   PHE A 432 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL A 332 " --> pdb=" O   PHE A 432 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ASN A 297 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLU A 333 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL A 299 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA A 451 " --> pdb=" O   TRP A 474 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL A 473 " --> pdb=" O   ARG B 514 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LYS B 516 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE A 475 " --> pdb=" O   LYS B 516 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER B 175 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER C 175 " --> pdb=" O   ILE C 167 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA D 451 " --> pdb=" O   TRP D 474 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ASN D 297 " --> pdb=" O   TYR D 331 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLU D 333 " --> pdb=" O   ASN D 297 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL D 299 " --> pdb=" O   GLU D 333 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   VAL D 330 " --> pdb=" O   THR D 430 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   PHE D 432 " --> pdb=" O   VAL D 330 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL D 332 " --> pdb=" O   PHE D 432 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   VAL D 407 " --> pdb=" O   ILE D 390 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35
    Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 49
    Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 65
      removed outlier: 7.179A  pdb=" N   LYS B  60 " --> pdb=" O   TYR B  77 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   TYR B  77 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE B  62 " --> pdb=" O   HIS B  75 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   HIS B  75 " --> pdb=" O   PHE B  62 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL B  64 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 245
      removed outlier: 6.607A  pdb=" N   CYS B 185 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   LYS B 215 " --> pdb=" O   CYS B 185 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLN B 187 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS B 263 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   THR B 267 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 35
    Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 49
    Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 65
      removed outlier: 7.179A  pdb=" N   LYS C  60 " --> pdb=" O   TYR C  77 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   TYR C  77 " --> pdb=" O   LYS C  60 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE C  62 " --> pdb=" O   HIS C  75 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   HIS C  75 " --> pdb=" O   PHE C  62 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL C  64 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 241 through 245
      removed outlier: 6.606A  pdb=" N   CYS C 185 " --> pdb=" O   VAL C 213 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   LYS C 215 " --> pdb=" O   CYS C 185 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLN C 187 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS C 263 " --> pdb=" O   VAL C 184 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   THR C 267 " --> pdb=" O   ILE C 188 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 30 through 35
    Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 49
    Processing sheet with id=AB8, first strand: chain 'D' and resid 60 through 65
      removed outlier: 7.179A  pdb=" N   LYS D  60 " --> pdb=" O   TYR D  77 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   TYR D  77 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE D  62 " --> pdb=" O   HIS D  75 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   HIS D  75 " --> pdb=" O   PHE D  62 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL D  64 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 241 through 245
      removed outlier: 6.607A  pdb=" N   CYS D 185 " --> pdb=" O   VAL D 213 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   LYS D 215 " --> pdb=" O   CYS D 185 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   GLN D 187 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS D 263 " --> pdb=" O   VAL D 184 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   THR D 267 " --> pdb=" O   ILE D 188 " (cutoff:3.500A)

    720 hydrogen bonds defined for protein.
    2016 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.71

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 2746
        1.31 -     1.45: 4703
        1.45 -     1.59: 8191
        1.59 -     1.73: 24
        1.73 -     1.87: 72
  Bond restraints: 15736
  Sorted by residual:
  bond pdb=" C1D NAP D 601 "
       pdb=" O4D NAP D 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.570 -0.195 2.00e-02 2.50e+03 9.49e+01
  bond pdb=" C1D NAP C 601 "
       pdb=" O4D NAP C 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.570 -0.195 2.00e-02 2.50e+03 9.47e+01
  bond pdb=" C1D NAP B 601 "
       pdb=" O4D NAP B 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.569 -0.194 2.00e-02 2.50e+03 9.41e+01
  bond pdb=" C1D NAP A 601 "
       pdb=" O4D NAP A 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.569 -0.194 2.00e-02 2.50e+03 9.40e+01
  bond pdb=" C1B NAP A 601 "
       pdb=" O4B NAP A 601 "
    ideal  model  delta    sigma   weight residual
    1.400  1.564 -0.164 2.00e-02 2.50e+03 6.75e+01
  ... (remaining 15731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 18111
        2.28 -     4.55: 2647
        4.55 -     6.83: 473
        6.83 -     9.11: 113
        9.11 -    11.39: 16
  Bond angle restraints: 21360
  Sorted by residual:
  angle pdb=" N   PHE D 490 "
        pdb=" CA  PHE D 490 "
        pdb=" C   PHE D 490 "
      ideal   model   delta    sigma   weight residual
     111.07  120.82   -9.75 1.07e+00 8.73e-01 8.30e+01
  angle pdb=" N   PHE C 490 "
        pdb=" CA  PHE C 490 "
        pdb=" C   PHE C 490 "
      ideal   model   delta    sigma   weight residual
     111.07  120.80   -9.73 1.07e+00 8.73e-01 8.26e+01
  angle pdb=" N   PHE B 490 "
        pdb=" CA  PHE B 490 "
        pdb=" C   PHE B 490 "
      ideal   model   delta    sigma   weight residual
     111.07  120.79   -9.72 1.07e+00 8.73e-01 8.26e+01
  angle pdb=" N   PHE A 490 "
        pdb=" CA  PHE A 490 "
        pdb=" C   PHE A 490 "
      ideal   model   delta    sigma   weight residual
     111.07  120.78   -9.71 1.07e+00 8.73e-01 8.24e+01
  angle pdb=" CA  PHE B 432 "
        pdb=" CB  PHE B 432 "
        pdb=" CG  PHE B 432 "
      ideal   model   delta    sigma   weight residual
     113.80  121.66   -7.86 1.00e+00 1.00e+00 6.17e+01
  ... (remaining 21355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 8946
       16.91 -    33.82: 362
       33.82 -    50.73: 130
       50.73 -    67.65: 98
       67.65 -    84.56: 28
  Dihedral angle restraints: 9564
    sinusoidal: 3912
      harmonic: 5652
  Sorted by residual:
  dihedral pdb=" N   PHE A 174 "
           pdb=" C   PHE A 174 "
           pdb=" CA  PHE A 174 "
           pdb=" CB  PHE A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.63   15.17     0      2.50e+00 1.60e-01 3.68e+01
  dihedral pdb=" N   PHE B 174 "
           pdb=" C   PHE B 174 "
           pdb=" CA  PHE B 174 "
           pdb=" CB  PHE B 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.66   15.14     0      2.50e+00 1.60e-01 3.67e+01
  dihedral pdb=" N   PHE C 174 "
           pdb=" C   PHE C 174 "
           pdb=" CA  PHE C 174 "
           pdb=" CB  PHE C 174 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.66   15.14     0      2.50e+00 1.60e-01 3.67e+01
  ... (remaining 9561 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1650
       0.095 -    0.190: 617
       0.190 -    0.285: 114
       0.285 -    0.380: 15
       0.380 -    0.475: 4
  Chirality restraints: 2400
  Sorted by residual:
  chirality pdb=" CA  TYR C 176 "
            pdb=" N   TYR C 176 "
            pdb=" C   TYR C 176 "
            pdb=" CB  TYR C 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CA  TYR B 176 "
            pdb=" N   TYR B 176 "
            pdb=" C   TYR B 176 "
            pdb=" CB  TYR B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.60e+00
  chirality pdb=" CA  TYR D 176 "
            pdb=" N   TYR D 176 "
            pdb=" C   TYR D 176 "
            pdb=" CB  TYR D 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.58e+00
  ... (remaining 2397 not shown)

  Planarity restraints: 2744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 519 "   -0.027 2.00e-02 2.50e+03   5.40e-02 2.92e+01
        pdb=" C   GLU B 519 "    0.093 2.00e-02 2.50e+03
        pdb=" O   GLU B 519 "   -0.034 2.00e-02 2.50e+03
        pdb=" OXT GLU B 519 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 519 "    0.027 2.00e-02 2.50e+03   5.39e-02 2.91e+01
        pdb=" C   GLU C 519 "   -0.093 2.00e-02 2.50e+03
        pdb=" O   GLU C 519 "    0.033 2.00e-02 2.50e+03
        pdb=" OXT GLU C 519 "    0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 519 "   -0.027 2.00e-02 2.50e+03   5.37e-02 2.89e+01
        pdb=" C   GLU A 519 "    0.093 2.00e-02 2.50e+03
        pdb=" O   GLU A 519 "   -0.033 2.00e-02 2.50e+03
        pdb=" OXT GLU A 519 "   -0.033 2.00e-02 2.50e+03
  ... (remaining 2741 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 3468
        2.77 -     3.31: 14724
        3.31 -     3.84: 24282
        3.84 -     4.37: 29523
        4.37 -     4.90: 48523
  Nonbonded interactions: 120520
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 307 "
            pdb=" OD2 ASP D 518 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OE1 GLU D 218 "
            pdb=" O3X NAP D 601 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE1 GLU C 218 "
            pdb=" O3X NAP C 601 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE1 GLU A 218 "
            pdb=" O3X NAP A 601 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OE1 GLU B 218 "
            pdb=" O3X NAP B 601 "
     model   vdw
     2.304 3.040
  ... (remaining 120515 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.820
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
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      :  0.020   0.195  15736  Z= 1.084
  Angle     :  1.766  11.387  21360  Z= 1.169
  Chirality :  0.097   0.475   2400
  Planarity :  0.008   0.054   2744
  Dihedral  : 13.757  84.557   5956
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.19), residues: 1972
  helix: -0.34 (0.18), residues: 736
  sheet:  0.51 (0.23), residues: 432
  loop :  0.71 (0.25), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 497 
 TYR   0.034   0.008   TYR A 230 
 PHE   0.027   0.006   PHE C  48 
 TRP   0.043   0.011   TRP D 100 
 HIS   0.010   0.003   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01999 (15736)
  covalent geometry    : angle       1.76599 (21360)
  hydrogen bonds       : bond        0.21764 (  720)
  hydrogen bonds       : angle       7.64217 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  556 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 556
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7907 (mm) cc_final: 0.7668 (mt)
REVERT: A   75 HIS cc_start: 0.7077 (m-70) cc_final: 0.6497 (m170)
REVERT: A   89 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6634 (mm-40)
REVERT: A  161 LYS cc_start: 0.6823 (mmtm) cc_final: 0.5848 (mtpt)
REVERT: A  428 THR cc_start: 0.8162 (m) cc_final: 0.7914 (p)
REVERT: A  446 GLU cc_start: 0.6794 (mp0) cc_final: 0.6141 (pm20)
REVERT: A  498 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6617 (mt-10)
REVERT: B   75 HIS cc_start: 0.7260 (m-70) cc_final: 0.6801 (m170)
REVERT: B   80 ARG cc_start: 0.6485 (mmm-85) cc_final: 0.4805 (mmm-85)
REVERT: B   89 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6674 (mp10)
REVERT: B  161 LYS cc_start: 0.6653 (mmtm) cc_final: 0.6127 (mtpt)
REVERT: B  166 MET cc_start: 0.7972 (tpt) cc_final: 0.7363 (tpp)
REVERT: B  343 GLU cc_start: 0.7840 (tp30) cc_final: 0.7495 (tp30)
REVERT: B  428 THR cc_start: 0.8113 (m) cc_final: 0.7853 (p)
REVERT: B  446 GLU cc_start: 0.6696 (mp0) cc_final: 0.6123 (pm20)
REVERT: B  498 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6624 (mt-10)
REVERT: C   29 MET cc_start: 0.5882 (mmp) cc_final: 0.5636 (tmm)
REVERT: C   63 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6431 (mt-10)
REVERT: C   83 ASP cc_start: 0.6601 (m-30) cc_final: 0.6305 (m-30)
REVERT: C  138 ILE cc_start: 0.8060 (tp) cc_final: 0.7787 (tp)
REVERT: C  253 GLU cc_start: 0.7613 (mt-10) cc_final: 0.6950 (mm-30)
REVERT: C  297 ASN cc_start: 0.8539 (m-40) cc_final: 0.7918 (m-40)
REVERT: C  369 GLN cc_start: 0.7175 (pm20) cc_final: 0.6677 (tt0)
REVERT: C  497 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7391 (mpt180)
REVERT: C  498 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6994 (mm-30)
REVERT: C  504 LEU cc_start: 0.7849 (mt) cc_final: 0.7343 (tp)
REVERT: D   29 MET cc_start: 0.5608 (mmp) cc_final: 0.5167 (tmm)
REVERT: D   40 GLU cc_start: 0.6561 (tp30) cc_final: 0.6175 (pm20)
REVERT: D   65 ILE cc_start: 0.7817 (mm) cc_final: 0.7499 (tt)
REVERT: D   83 ASP cc_start: 0.6808 (m-30) cc_final: 0.6556 (m-30)
REVERT: D  138 ILE cc_start: 0.8088 (tp) cc_final: 0.7819 (tp)
REVERT: D  213 VAL cc_start: 0.8532 (t) cc_final: 0.8094 (p)
REVERT: D  250 ILE cc_start: 0.6942 (mt) cc_final: 0.6742 (mm)
REVERT: D  275 HIS cc_start: 0.6644 (t70) cc_final: 0.6185 (t-170)
REVERT: D  369 GLN cc_start: 0.7198 (pm20) cc_final: 0.6737 (tp40)
REVERT: D  428 THR cc_start: 0.7965 (m) cc_final: 0.7761 (p)
REVERT: D  431 LYS cc_start: 0.7087 (mttt) cc_final: 0.6698 (ptmt)
  outliers start: 0
  outliers final: 0
  residues processed: 556
  average time/residue: 0.1375
  time to fit residues: 110.6487
Evaluate side-chains
  256 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 134 ASN
A 371 GLN
A 483 HIS
A 491 ASN
B  43 GLN
B  58 GLN
B 371 GLN
B 483 HIS
B 491 ASN
C 363 GLN
C 384 ASN
C 491 ASN
D 297 ASN
D 491 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.152513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.131743 restraints weight = 20971.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.132487 restraints weight = 18255.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.134382 restraints weight = 15620.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.134936 restraints weight = 11951.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.135250 restraints weight = 10715.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15736  Z= 0.168
  Angle     :  0.669   7.633  21360  Z= 0.371
  Chirality :  0.047   0.239   2400
  Planarity :  0.005   0.037   2744
  Dihedral  : 12.789  80.806   2376
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 11.25 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.20), residues: 1972
  helix:  0.90 (0.19), residues: 740
  sheet:  0.82 (0.23), residues: 468
  loop :  0.30 (0.25), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 114 
 TYR   0.020   0.002   TYR A 176 
 PHE   0.026   0.002   PHE C 340 
 TRP   0.019   0.002   TRP D 198 
 HIS   0.006   0.001   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (15736)
  covalent geometry    : angle       0.66926 (21360)
  hydrogen bonds       : bond        0.06170 (  720)
  hydrogen bonds       : angle       5.38425 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 294
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7631 (mm) cc_final: 0.7424 (mt)
REVERT: A  134 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6598 (m110)
REVERT: A  179 ARG cc_start: 0.8203 (mtt-85) cc_final: 0.7984 (mtt180)
REVERT: A  289 LEU cc_start: 0.7973 (pp) cc_final: 0.7553 (mt)
REVERT: A  338 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5680 (t70)
REVERT: B  161 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7580 (tptp)
REVERT: B  166 MET cc_start: 0.7758 (tpt) cc_final: 0.7217 (tpp)
REVERT: B  179 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7882 (mtt180)
REVERT: B  338 ASP cc_start: 0.6000 (OUTLIER) cc_final: 0.5708 (t0)
REVERT: C  213 VAL cc_start: 0.8775 (t) cc_final: 0.8495 (p)
REVERT: C  253 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6917 (mm-30)
REVERT: C  275 HIS cc_start: 0.7611 (m-70) cc_final: 0.6914 (t70)
REVERT: C  297 ASN cc_start: 0.8841 (m-40) cc_final: 0.8406 (m-40)
REVERT: C  431 LYS cc_start: 0.6683 (mttt) cc_final: 0.6453 (ptmm)
REVERT: D   29 MET cc_start: 0.5831 (mmp) cc_final: 0.5380 (tmm)
REVERT: D   41 TYR cc_start: 0.4386 (t80) cc_final: 0.3864 (t80)
REVERT: D  213 VAL cc_start: 0.8853 (t) cc_final: 0.8601 (p)
REVERT: D  316 ILE cc_start: 0.8477 (tp) cc_final: 0.8272 (tp)
REVERT: D  351 ILE cc_start: 0.7497 (tp) cc_final: 0.7156 (mt)
REVERT: D  406 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6916 (p)
REVERT: D  415 MET cc_start: 0.7997 (mtp) cc_final: 0.7737 (ttp)
  outliers start: 47
  outliers final: 25
  residues processed: 331
  average time/residue: 0.1215
  time to fit residues: 60.5240
Evaluate side-chains
  237 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  134 ASN
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  225 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  510 VAL
Chi-restraints excluded: chain D residue  225 LEU
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  297 ASN
Chi-restraints excluded: chain D residue  406 THR
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  493 SER
Chi-restraints excluded: chain D residue  510 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 179 optimal weight:   10.0000
   chunk 192 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 194 optimal weight:    0.1980
   chunk 45 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 176 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 111 optimal weight:   10.0000
   chunk 184 optimal weight:    8.9990
   overall best weight:    5.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 192 ASN
A 454 HIS
A 469 ASN
B 134 ASN
B 192 ASN
B 242 ASN
B 454 HIS
B 469 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.138392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.118084 restraints weight = 22116.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.118891 restraints weight = 18237.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.120573 restraints weight = 15537.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120964 restraints weight = 12272.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.121325 restraints weight = 11494.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.078  15736  Z= 0.381
  Angle     :  0.909   9.161  21360  Z= 0.504
  Chirality :  0.056   0.220   2400
  Planarity :  0.007   0.065   2744
  Dihedral  : 12.558  85.343   2376
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 15.89 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.18), residues: 1972
  helix:  0.15 (0.18), residues: 772
  sheet:  0.20 (0.24), residues: 452
  loop : -1.25 (0.22), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 329 
 TYR   0.047   0.004   TYR C 230 
 PHE   0.033   0.004   PHE A 193 
 TRP   0.015   0.003   TRP A 200 
 HIS   0.012   0.002   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00911 (15736)
  covalent geometry    : angle       0.90941 (21360)
  hydrogen bonds       : bond        0.08795 (  720)
  hydrogen bonds       : angle       5.79099 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 225
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7801 (mm) cc_final: 0.7505 (mt)
REVERT: A  161 LYS cc_start: 0.8216 (mptt) cc_final: 0.7911 (mppt)
REVERT: A  179 ARG cc_start: 0.8389 (mtt-85) cc_final: 0.8138 (mtt180)
REVERT: A  337 TYR cc_start: 0.7506 (t80) cc_final: 0.7095 (t80)
REVERT: A  463 LYS cc_start: 0.7741 (tttt) cc_final: 0.7503 (ttpt)
REVERT: B  134 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.6574 (m110)
REVERT: B  166 MET cc_start: 0.8330 (tpt) cc_final: 0.8028 (tpp)
REVERT: B  179 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.8142 (mtt180)
REVERT: B  463 LYS cc_start: 0.7931 (tttt) cc_final: 0.7598 (ttpt)
REVERT: C   65 ILE cc_start: 0.7854 (mm) cc_final: 0.7475 (tt)
REVERT: C  136 LYS cc_start: 0.7243 (tttp) cc_final: 0.7029 (mtpt)
REVERT: C  253 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7245 (mm-30)
REVERT: C  310 GLN cc_start: 0.6613 (mm-40) cc_final: 0.6317 (tm-30)
REVERT: C  369 GLN cc_start: 0.7551 (pm20) cc_final: 0.6647 (tm-30)
REVERT: C  431 LYS cc_start: 0.7356 (mttt) cc_final: 0.7125 (ptmm)
REVERT: D  130 GLU cc_start: 0.7467 (tp30) cc_final: 0.7148 (tp30)
REVERT: D  166 MET cc_start: 0.7207 (tpp) cc_final: 0.5785 (tpp)
REVERT: D  278 GLN cc_start: 0.7579 (mm-40) cc_final: 0.6953 (mp10)
REVERT: D  369 GLN cc_start: 0.7322 (pm20) cc_final: 0.6507 (tm-30)
REVERT: D  431 LYS cc_start: 0.7734 (ptmt) cc_final: 0.7509 (ptmm)
  outliers start: 66
  outliers final: 46
  residues processed: 280
  average time/residue: 0.1222
  time to fit residues: 51.1722
Evaluate side-chains
  223 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 176
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  155 SER
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  502 ASP
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  134 ASN
Chi-restraints excluded: chain B residue  155 SER
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain C residue  264 VAL
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  295 SER
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  510 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   74 CYS
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  136 LYS
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  288 THR
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  510 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 147 optimal weight:   10.0000
   chunk 171 optimal weight:    5.9990
   chunk 138 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 183 optimal weight:    9.9990
   chunk 121 optimal weight:    0.6980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 242 ASN
B 469 ASN
D 310 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.142215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.121782 restraints weight = 21195.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.121870 restraints weight = 17678.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.124088 restraints weight = 15559.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.124652 restraints weight = 11750.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.124990 restraints weight = 10666.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.5490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15736  Z= 0.156
  Angle     :  0.585   7.407  21360  Z= 0.324
  Chirality :  0.046   0.187   2400
  Planarity :  0.005   0.052   2744
  Dihedral  : 10.771  81.684   2376
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 17.36 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.19), residues: 1972
  helix:  0.97 (0.19), residues: 748
  sheet:  0.26 (0.24), residues: 460
  loop : -1.13 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 467 
 TYR   0.017   0.002   TYR C 337 
 PHE   0.014   0.002   PHE A 193 
 TRP   0.010   0.002   TRP A 198 
 HIS   0.003   0.001   HIS D 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (15736)
  covalent geometry    : angle       0.58523 (21360)
  hydrogen bonds       : bond        0.05347 (  720)
  hydrogen bonds       : angle       5.06578 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 205
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7648 (mm) cc_final: 0.7398 (mt)
REVERT: A  337 TYR cc_start: 0.7556 (t80) cc_final: 0.7015 (t80)
REVERT: B  166 MET cc_start: 0.8256 (tpt) cc_final: 0.7790 (tpp)
REVERT: B  276 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (mm)
REVERT: C   65 ILE cc_start: 0.7897 (mm) cc_final: 0.7552 (tt)
REVERT: C  253 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6934 (mm-30)
REVERT: C  369 GLN cc_start: 0.7606 (pm20) cc_final: 0.6725 (tm-30)
REVERT: D   41 TYR cc_start: 0.5338 (t80) cc_final: 0.4644 (t80)
REVERT: D  129 ILE cc_start: 0.8923 (mt) cc_final: 0.8265 (mt)
REVERT: D  369 GLN cc_start: 0.7355 (pm20) cc_final: 0.6270 (tm-30)
  outliers start: 61
  outliers final: 35
  residues processed: 248
  average time/residue: 0.1194
  time to fit residues: 45.2129
Evaluate side-chains
  212 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 176
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  368 SER
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  510 VAL
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  411 VAL
Chi-restraints excluded: chain D residue  510 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 156 optimal weight:    7.9990
   chunk 169 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0870
   chunk 136 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 95 optimal weight:    7.9990
   chunk 81 optimal weight:    6.9990
   overall best weight:    1.1160

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

Flipped N/Q/H residues before XYZ refinement:
A 366 GLN
D 278 GLN
D 310 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.145707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.125499 restraints weight = 20944.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.126434 restraints weight = 16850.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.127701 restraints weight = 14541.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127928 restraints weight = 11933.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.128669 restraints weight = 11271.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.5705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15736  Z= 0.122
  Angle     :  0.518   5.211  21360  Z= 0.287
  Chirality :  0.044   0.318   2400
  Planarity :  0.004   0.048   2744
  Dihedral  :  9.139  74.587   2376
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.01 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.19), residues: 1972
  helix:  1.32 (0.20), residues: 752
  sheet:  0.49 (0.24), residues: 460
  loop : -1.05 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 467 
 TYR   0.016   0.002   TYR C 337 
 PHE   0.012   0.001   PHE A 432 
 TRP   0.009   0.001   TRP C 198 
 HIS   0.003   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (15736)
  covalent geometry    : angle       0.51781 (21360)
  hydrogen bonds       : bond        0.04411 (  720)
  hydrogen bonds       : angle       4.80513 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 203
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7761 (mm) cc_final: 0.7351 (mt)
REVERT: A  337 TYR cc_start: 0.7493 (t80) cc_final: 0.6985 (t80)
REVERT: A  463 LYS cc_start: 0.7497 (tttp) cc_final: 0.6921 (ttpt)
REVERT: B  166 MET cc_start: 0.8001 (tpt) cc_final: 0.7480 (tpp)
REVERT: B  276 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8580 (mm)
REVERT: C   65 ILE cc_start: 0.7885 (mm) cc_final: 0.7552 (tt)
REVERT: C  253 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6887 (mm-30)
REVERT: C  369 GLN cc_start: 0.7484 (pm20) cc_final: 0.6590 (tm-30)
REVERT: D   41 TYR cc_start: 0.5336 (t80) cc_final: 0.4625 (t80)
REVERT: D  129 ILE cc_start: 0.8949 (mt) cc_final: 0.8484 (mt)
REVERT: D  369 GLN cc_start: 0.7327 (pm20) cc_final: 0.6255 (tm-30)
  outliers start: 46
  outliers final: 29
  residues processed: 232
  average time/residue: 0.1222
  time to fit residues: 42.9978
Evaluate side-chains
  215 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  368 SER
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  415 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 175 optimal weight:    0.3980
   chunk 55 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 191 optimal weight:    7.9990
   chunk 181 optimal weight:    0.6980
   chunk 82 optimal weight:   10.0000
   chunk 123 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 139 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 132 optimal weight:    7.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
D 278 GLN
D 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.140520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.121102 restraints weight = 21614.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.121465 restraints weight = 16719.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.122238 restraints weight = 15428.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.122970 restraints weight = 13182.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.123279 restraints weight = 11775.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.5896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  15736  Z= 0.179
  Angle     :  0.582   5.321  21360  Z= 0.319
  Chirality :  0.046   0.193   2400
  Planarity :  0.005   0.050   2744
  Dihedral  :  8.992  74.738   2376
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.44 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.19), residues: 1972
  helix:  1.22 (0.19), residues: 752
  sheet:  0.31 (0.24), residues: 452
  loop : -1.23 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 395 
 TYR   0.019   0.002   TYR C 230 
 PHE   0.017   0.002   PHE A 193 
 TRP   0.009   0.002   TRP C 474 
 HIS   0.005   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (15736)
  covalent geometry    : angle       0.58171 (21360)
  hydrogen bonds       : bond        0.05296 (  720)
  hydrogen bonds       : angle       4.94151 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 197
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7922 (mm) cc_final: 0.7597 (mt)
REVERT: A  166 MET cc_start: 0.7814 (tpp) cc_final: 0.7147 (ttm)
REVERT: A  337 TYR cc_start: 0.7558 (t80) cc_final: 0.7049 (t80)
REVERT: A  383 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6249 (ttpp)
REVERT: B  166 MET cc_start: 0.8209 (tpt) cc_final: 0.7446 (tpp)
REVERT: B  276 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8595 (mm)
REVERT: C   65 ILE cc_start: 0.7831 (mm) cc_final: 0.7517 (tt)
REVERT: C  253 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6924 (mm-30)
REVERT: C  369 GLN cc_start: 0.7472 (pm20) cc_final: 0.6625 (tm-30)
REVERT: D   41 TYR cc_start: 0.5522 (t80) cc_final: 0.4758 (t80)
REVERT: D   78 GLU cc_start: 0.6119 (tp30) cc_final: 0.5796 (tp30)
REVERT: D  129 ILE cc_start: 0.8960 (mt) cc_final: 0.8526 (mt)
REVERT: D  369 GLN cc_start: 0.7384 (pm20) cc_final: 0.6135 (tm-30)
  outliers start: 55
  outliers final: 42
  residues processed: 236
  average time/residue: 0.1211
  time to fit residues: 43.8153
Evaluate side-chains
  221 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 177
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  383 LYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  422 ILE
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  368 SER
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  441 MET
Chi-restraints excluded: chain D residue  517 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 184 optimal weight:    5.9990
   chunk 168 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0770
   chunk 114 optimal weight:    2.9990
   chunk 180 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 49 optimal weight:   10.0000
   chunk 182 optimal weight:    4.9990
   overall best weight:    1.3344

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

Flipped N/Q/H residues before XYZ refinement:
B 366 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.144640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.124642 restraints weight = 20851.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.125146 restraints weight = 17058.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.126229 restraints weight = 15518.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.126514 restraints weight = 12945.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.128014 restraints weight = 12005.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.6034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  15736  Z= 0.127
  Angle     :  0.509   5.211  21360  Z= 0.281
  Chirality :  0.044   0.158   2400
  Planarity :  0.004   0.047   2744
  Dihedral  :  8.463  72.125   2376
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.99 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.19), residues: 1972
  helix:  1.39 (0.20), residues: 752
  sheet:  0.40 (0.24), residues: 460
  loop : -1.16 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 467 
 TYR   0.014   0.002   TYR B 176 
 PHE   0.013   0.001   PHE B 432 
 TRP   0.010   0.001   TRP A 198 
 HIS   0.002   0.001   HIS C 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (15736)
  covalent geometry    : angle       0.50918 (21360)
  hydrogen bonds       : bond        0.04373 (  720)
  hydrogen bonds       : angle       4.75868 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 196
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7890 (mm) cc_final: 0.7388 (mt)
REVERT: A  166 MET cc_start: 0.7678 (tpp) cc_final: 0.7259 (ttm)
REVERT: A  337 TYR cc_start: 0.7547 (t80) cc_final: 0.7012 (t80)
REVERT: B   63 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6525 (tt0)
REVERT: B  276 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8598 (mm)
REVERT: B  467 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5845 (tpt170)
REVERT: C   65 ILE cc_start: 0.7840 (mm) cc_final: 0.7527 (tt)
REVERT: C  369 GLN cc_start: 0.7316 (pm20) cc_final: 0.6616 (tm-30)
REVERT: C  404 LYS cc_start: 0.7995 (mttm) cc_final: 0.7593 (mttt)
REVERT: D   41 TYR cc_start: 0.5390 (t80) cc_final: 0.4602 (t80)
REVERT: D  129 ILE cc_start: 0.8914 (mt) cc_final: 0.8420 (mt)
REVERT: D  278 GLN cc_start: 0.7004 (mm110) cc_final: 0.6776 (tt0)
REVERT: D  310 GLN cc_start: 0.6731 (mm-40) cc_final: 0.6504 (tm-30)
REVERT: D  369 GLN cc_start: 0.7301 (pm20) cc_final: 0.6064 (tm-30)
  outliers start: 46
  outliers final: 40
  residues processed: 225
  average time/residue: 0.1218
  time to fit residues: 42.1691
Evaluate side-chains
  225 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  418 VAL
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  467 ARG
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  441 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 189 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 114 optimal weight:    0.5980
   chunk 169 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 134 optimal weight:   10.0000
   chunk 187 optimal weight:    6.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.140827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.121478 restraints weight = 21804.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.121916 restraints weight = 16939.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.122806 restraints weight = 14995.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.123037 restraints weight = 12909.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.124759 restraints weight = 12170.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.6157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15736  Z= 0.162
  Angle     :  0.548   5.032  21360  Z= 0.301
  Chirality :  0.045   0.164   2400
  Planarity :  0.005   0.052   2744
  Dihedral  :  8.437  72.588   2376
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.38 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.19), residues: 1972
  helix:  1.31 (0.19), residues: 752
  sheet:  0.33 (0.24), residues: 456
  loop : -1.21 (0.22), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 467 
 TYR   0.018   0.002   TYR B 277 
 PHE   0.016   0.002   PHE A 193 
 TRP   0.008   0.002   TRP B 198 
 HIS   0.004   0.001   HIS A 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (15736)
  covalent geometry    : angle       0.54801 (21360)
  hydrogen bonds       : bond        0.04942 (  720)
  hydrogen bonds       : angle       4.87033 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 192
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7818 (mm) cc_final: 0.7523 (mt)
REVERT: A  166 MET cc_start: 0.7837 (tpp) cc_final: 0.7289 (ttm)
REVERT: A  289 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (pp)
REVERT: A  337 TYR cc_start: 0.7643 (t80) cc_final: 0.7117 (t80)
REVERT: A  383 LYS cc_start: 0.6613 (OUTLIER) cc_final: 0.6260 (ttpp)
REVERT: A  432 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6471 (t80)
REVERT: B   63 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6469 (tt0)
REVERT: B  166 MET cc_start: 0.8122 (tpp) cc_final: 0.7420 (tpp)
REVERT: B  276 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8601 (mm)
REVERT: B  467 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.5806 (tpt170)
REVERT: C   65 ILE cc_start: 0.7854 (mm) cc_final: 0.7539 (tt)
REVERT: C  369 GLN cc_start: 0.7285 (pm20) cc_final: 0.6531 (tm-30)
REVERT: D   41 TYR cc_start: 0.5493 (t80) cc_final: 0.4625 (t80)
REVERT: D  129 ILE cc_start: 0.8925 (mt) cc_final: 0.8400 (mt)
REVERT: D  278 GLN cc_start: 0.7251 (mm110) cc_final: 0.6911 (tt0)
REVERT: D  310 GLN cc_start: 0.6771 (mm-40) cc_final: 0.6511 (tm-30)
REVERT: D  369 GLN cc_start: 0.7346 (pm20) cc_final: 0.5959 (tm-30)
  outliers start: 55
  outliers final: 46
  residues processed: 232
  average time/residue: 0.1184
  time to fit residues: 42.8631
Evaluate side-chains
  230 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 178
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  383 LYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  124 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  467 ARG
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  441 MET
Chi-restraints excluded: chain D residue  493 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 168 optimal weight:    0.9990
   chunk 171 optimal weight:    9.9990
   chunk 133 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 170 optimal weight:    0.0770
   chunk 136 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 140 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   overall best weight:    1.2146

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.145055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.125402 restraints weight = 20829.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.125992 restraints weight = 15935.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.126758 restraints weight = 14730.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127748 restraints weight = 12351.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.127927 restraints weight = 10888.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.6233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15736  Z= 0.118
  Angle     :  0.502   8.704  21360  Z= 0.275
  Chirality :  0.044   0.158   2400
  Planarity :  0.004   0.050   2744
  Dihedral  :  8.094  70.064   2376
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.99 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.20), residues: 1972
  helix:  1.64 (0.20), residues: 724
  sheet:  0.43 (0.25), residues: 456
  loop : -0.98 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 467 
 TYR   0.013   0.001   TYR A 176 
 PHE   0.012   0.001   PHE B 432 
 TRP   0.015   0.001   TRP A 198 
 HIS   0.008   0.001   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (15736)
  covalent geometry    : angle       0.50153 (21360)
  hydrogen bonds       : bond        0.04132 (  720)
  hydrogen bonds       : angle       4.69408 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 192
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.7855 (mm) cc_final: 0.7529 (mt)
REVERT: A  166 MET cc_start: 0.7664 (tpp) cc_final: 0.7227 (ttm)
REVERT: A  289 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7987 (pp)
REVERT: A  337 TYR cc_start: 0.7614 (t80) cc_final: 0.7068 (t80)
REVERT: B   63 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6522 (tt0)
REVERT: B  166 MET cc_start: 0.8037 (tpp) cc_final: 0.7611 (tpp)
REVERT: B  276 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8595 (mm)
REVERT: B  467 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6052 (tpt170)
REVERT: C   65 ILE cc_start: 0.7862 (mm) cc_final: 0.7567 (tt)
REVERT: C  369 GLN cc_start: 0.7247 (pm20) cc_final: 0.6610 (tm-30)
REVERT: D   41 TYR cc_start: 0.5423 (t80) cc_final: 0.4566 (t80)
REVERT: D  129 ILE cc_start: 0.8865 (mt) cc_final: 0.8357 (mt)
REVERT: D  278 GLN cc_start: 0.7198 (mm110) cc_final: 0.6875 (tt0)
REVERT: D  310 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6481 (tm-30)
  outliers start: 53
  outliers final: 42
  residues processed: 229
  average time/residue: 0.1124
  time to fit residues: 40.2646
Evaluate side-chains
  227 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 181
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  218 GLU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  467 ARG
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  338 ASP
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain C residue  505 GLN
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  338 ASP
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  441 MET
Chi-restraints excluded: chain D residue  493 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 134 optimal weight:   20.0000
   chunk 179 optimal weight:    4.9990
   chunk 130 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 176 optimal weight:    8.9990
   chunk 29 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
A 469 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.134326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.114884 restraints weight = 22142.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.115763 restraints weight = 18416.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.117124 restraints weight = 16373.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.117705 restraints weight = 12839.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.117995 restraints weight = 11372.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.6473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.071  15736  Z= 0.364
  Angle     :  0.816   8.636  21360  Z= 0.442
  Chirality :  0.053   0.189   2400
  Planarity :  0.007   0.064   2744
  Dihedral  :  9.757  80.514   2376
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.80 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.18), residues: 1972
  helix:  0.68 (0.19), residues: 748
  sheet: -0.52 (0.24), residues: 464
  loop : -1.77 (0.21), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  93 
 TYR   0.040   0.004   TYR B 277 
 PHE   0.027   0.003   PHE B 193 
 TRP   0.022   0.003   TRP C 474 
 HIS   0.010   0.002   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00883 (15736)
  covalent geometry    : angle       0.81629 (21360)
  hydrogen bonds       : bond        0.07911 (  720)
  hydrogen bonds       : angle       5.64129 ( 2016)

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

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

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3944 Ramachandran restraints generated.
    1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 170
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.8065 (mm) cc_final: 0.7813 (mt)
REVERT: A  289 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8159 (pp)
REVERT: A  337 TYR cc_start: 0.7772 (t80) cc_final: 0.7264 (t80)
REVERT: A  358 ASP cc_start: 0.5365 (t0) cc_final: 0.3336 (m-30)
REVERT: A  383 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6280 (ttpp)
REVERT: A  432 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6336 (t80)
REVERT: B   63 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6600 (tt0)
REVERT: B  428 THR cc_start: 0.8969 (m) cc_final: 0.8701 (p)
REVERT: B  432 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6345 (t80)
REVERT: C   65 ILE cc_start: 0.8033 (mm) cc_final: 0.7596 (tt)
REVERT: C  369 GLN cc_start: 0.7273 (pm20) cc_final: 0.6563 (tm-30)
REVERT: D   41 TYR cc_start: 0.5833 (t80) cc_final: 0.4989 (t80)
REVERT: D  129 ILE cc_start: 0.8892 (mt) cc_final: 0.8306 (mt)
REVERT: D  166 MET cc_start: 0.7494 (tpp) cc_final: 0.7060 (tpt)
REVERT: D  278 GLN cc_start: 0.7410 (mm110) cc_final: 0.7140 (tt0)
REVERT: D  369 GLN cc_start: 0.7466 (pm20) cc_final: 0.6190 (tm-30)
  outliers start: 62
  outliers final: 45
  residues processed: 216
  average time/residue: 0.1109
  time to fit residues: 37.5998
Evaluate side-chains
  217 residues out of total 1636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 167
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  124 ASP
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  383 LYS
Chi-restraints excluded: chain A residue  411 VAL
Chi-restraints excluded: chain A residue  432 PHE
Chi-restraints excluded: chain A residue  449 LEU
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  219 SER
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  411 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  432 PHE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  499 MET
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   74 CYS
Chi-restraints excluded: chain C residue  119 ILE
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  163 ASP
Chi-restraints excluded: chain C residue  275 HIS
Chi-restraints excluded: chain C residue  276 ILE
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  438 VAL
Chi-restraints excluded: chain C residue  468 VAL
Chi-restraints excluded: chain C residue  493 SER
Chi-restraints excluded: chain D residue  119 ILE
Chi-restraints excluded: chain D residue  163 ASP
Chi-restraints excluded: chain D residue  276 ILE
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  295 SER
Chi-restraints excluded: chain D residue  343 GLU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  380 ASP
Chi-restraints excluded: chain D residue  438 VAL
Chi-restraints excluded: chain D residue  493 SER
Chi-restraints excluded: chain D residue  517 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 153 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 150 optimal weight:    8.9990
   chunk 126 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 176 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.143672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.124485 restraints weight = 21005.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.124958 restraints weight = 16100.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.125766 restraints weight = 14488.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.126621 restraints weight = 12547.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.126825 restraints weight = 11132.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.6464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  15736  Z= 0.120
  Angle     :  0.524   8.322  21360  Z= 0.290
  Chirality :  0.044   0.154   2400
  Planarity :  0.005   0.075   2744
  Dihedral  :  8.388  73.655   2376
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.03 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.19), residues: 1972
  helix:  1.23 (0.19), residues: 752
  sheet: -0.10 (0.24), residues: 464
  loop : -1.45 (0.21), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 416 
 TYR   0.014   0.001   TYR A 176 
 PHE   0.012   0.001   PHE B 432 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.003   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (15736)
  covalent geometry    : angle       0.52419 (21360)
  hydrogen bonds       : bond        0.04288 (  720)
  hydrogen bonds       : angle       4.83565 ( 2016)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2073.95 seconds
wall clock time: 36 minutes 57.06 seconds (2217.06 seconds total)