Starting phenix.real_space_refine
on Sat Aug 23 17:05:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8io3_35606/08_2025/8io3_35606.map"
  }
  resolution = 3.02
  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=   0.005 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      92      5.16       5
     C    8972      2.51       5
     N    2264      2.21       5
     O    2292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13620
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 3370
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3370
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 47}
          Link IDs: {'PTRANS': 16, 'TRANS': 415}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 181
          Unresolved non-hydrogen angles: 222
          Unresolved non-hydrogen dihedrals: 140
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 7, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 118
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'VXI': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    A, B, D
  Time building chain proxies: 2.64, per 1000 atoms: 0.19
  Number of scatterers: 13620
  At special positions: 0
  Unit cell: (122.558, 122.558, 112.038, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      92     16.00
     O    2292      8.00
     N    2264      7.00
     C    8972      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: 1.03
  Conformation dependent library (CDL) restraints added in 601.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3280

  Finding SS restraints...
    Secondary structure from input PDB file:
      88 helices and 8 sheets defined
      72.7% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'C' and resid 50 through 54
      removed outlier: 4.095A  pdb=" N   LEU C  53 " --> pdb=" O   GLY C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 58 through 66
    Processing helix  chain 'C' and resid 67 through 81
      removed outlier: 3.697A  pdb=" N   VAL C  71 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 117
      removed outlier: 3.771A  pdb=" N   PHE C  94 " --> pdb=" O   SER C  90 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE C  99 " --> pdb=" O   TYR C  95 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU C 102 " --> pdb=" O   LEU C  98 " (cutoff:3.500A)
      Proline residue:  C 112  - end of helix
    Processing helix  chain 'C' and resid 123 through 145
      removed outlier: 3.879A  pdb=" N   LEU C 141 " --> pdb=" O   PHE C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 172
      removed outlier: 3.505A  pdb=" N   THR C 166 " --> pdb=" O   ARG C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 181
      removed outlier: 3.724A  pdb=" N   ILE C 181 " --> pdb=" O   LEU C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 191
      removed outlier: 4.044A  pdb=" N   ILE C 186 " --> pdb=" O   PRO C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 206 through 218
    Processing helix  chain 'C' and resid 219 through 222
      removed outlier: 3.615A  pdb=" N   LEU C 222 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 219 through 222'
    Processing helix  chain 'C' and resid 223 through 238
      removed outlier: 3.702A  pdb=" N   ARG C 229 " --> pdb=" O   SER C 225 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 276
      removed outlier: 3.719A  pdb=" N   VAL C 249 " --> pdb=" O   ALA C 245 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS C 267 " --> pdb=" O   HIS C 263 " (cutoff:3.500A)
      Proline residue:  C 273  - end of helix
      removed outlier: 3.897A  pdb=" N   GLN C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 287
    Processing helix  chain 'C' and resid 293 through 310
    Processing helix  chain 'C' and resid 321 through 351
      removed outlier: 3.602A  pdb=" N   TRP C 326 " --> pdb=" O   MET C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 354
      No H-bonds generated for 'chain 'C' and resid 352 through 354'
    Processing helix  chain 'C' and resid 355 through 375
      removed outlier: 3.915A  pdb=" N   TYR C 360 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN C 361 " --> pdb=" O   ARG C 357 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS C 374 " --> pdb=" O   TYR C 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 377 through 393
    Processing helix  chain 'C' and resid 398 through 406
      removed outlier: 3.537A  pdb=" N   LEU C 403 " --> pdb=" O   GLU C 399 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU C 406 " --> pdb=" O   ILE C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 407 through 419
    Processing helix  chain 'C' and resid 434 through 443
    Processing helix  chain 'C' and resid 518 through 528
      removed outlier: 3.763A  pdb=" N   PHE C 522 " --> pdb=" O   SER C 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 54
      removed outlier: 4.095A  pdb=" N   LEU A  53 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 66
    Processing helix  chain 'A' and resid 67 through 81
      removed outlier: 3.697A  pdb=" N   VAL A  71 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 117
      removed outlier: 3.771A  pdb=" N   PHE A  94 " --> pdb=" O   SER A  90 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE A  99 " --> pdb=" O   TYR A  95 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      Proline residue:  A 112  - end of helix
    Processing helix  chain 'A' and resid 123 through 145
      removed outlier: 3.879A  pdb=" N   LEU A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 172
      removed outlier: 3.505A  pdb=" N   THR A 166 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 3.724A  pdb=" N   ILE A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 191
      removed outlier: 4.044A  pdb=" N   ILE A 186 " --> pdb=" O   PRO A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
    Processing helix  chain 'A' and resid 219 through 222
      removed outlier: 3.615A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 219 through 222'
    Processing helix  chain 'A' and resid 223 through 238
      removed outlier: 3.702A  pdb=" N   ARG A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 276
      removed outlier: 3.719A  pdb=" N   VAL A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS A 267 " --> pdb=" O   HIS A 263 " (cutoff:3.500A)
      Proline residue:  A 273  - end of helix
      removed outlier: 3.897A  pdb=" N   GLN A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 293 through 310
    Processing helix  chain 'A' and resid 321 through 351
      removed outlier: 3.602A  pdb=" N   TRP A 326 " --> pdb=" O   MET A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 354
      No H-bonds generated for 'chain 'A' and resid 352 through 354'
    Processing helix  chain 'A' and resid 355 through 375
      removed outlier: 3.915A  pdb=" N   TYR A 360 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN A 361 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS A 374 " --> pdb=" O   TYR A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 393
    Processing helix  chain 'A' and resid 398 through 406
      removed outlier: 3.537A  pdb=" N   LEU A 403 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 419
    Processing helix  chain 'A' and resid 434 through 443
    Processing helix  chain 'A' and resid 518 through 528
      removed outlier: 3.763A  pdb=" N   PHE A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
      removed outlier: 4.095A  pdb=" N   LEU B  53 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 66
    Processing helix  chain 'B' and resid 67 through 81
      removed outlier: 3.697A  pdb=" N   VAL B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 117
      removed outlier: 3.771A  pdb=" N   PHE B  94 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE B  99 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 123 through 145
      removed outlier: 3.879A  pdb=" N   LEU B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 172
      removed outlier: 3.505A  pdb=" N   THR B 166 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 181
      removed outlier: 3.724A  pdb=" N   ILE B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 191
      removed outlier: 4.044A  pdb=" N   ILE B 186 " --> pdb=" O   PRO B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 218
    Processing helix  chain 'B' and resid 219 through 222
      removed outlier: 3.615A  pdb=" N   LEU B 222 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 219 through 222'
    Processing helix  chain 'B' and resid 223 through 238
      removed outlier: 3.702A  pdb=" N   ARG B 229 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 276
      removed outlier: 3.719A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS B 267 " --> pdb=" O   HIS B 263 " (cutoff:3.500A)
      Proline residue:  B 273  - end of helix
      removed outlier: 3.897A  pdb=" N   GLN B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
    Processing helix  chain 'B' and resid 293 through 310
    Processing helix  chain 'B' and resid 321 through 351
      removed outlier: 3.602A  pdb=" N   TRP B 326 " --> pdb=" O   MET B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 354
      No H-bonds generated for 'chain 'B' and resid 352 through 354'
    Processing helix  chain 'B' and resid 355 through 375
      removed outlier: 3.915A  pdb=" N   TYR B 360 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN B 361 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS B 374 " --> pdb=" O   TYR B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 393
    Processing helix  chain 'B' and resid 398 through 406
      removed outlier: 3.537A  pdb=" N   LEU B 403 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 406 " --> pdb=" O   ILE B 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 419
    Processing helix  chain 'B' and resid 434 through 443
    Processing helix  chain 'B' and resid 518 through 528
      removed outlier: 3.763A  pdb=" N   PHE B 522 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 54
      removed outlier: 4.094A  pdb=" N   LEU D  53 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 66
    Processing helix  chain 'D' and resid 67 through 81
      removed outlier: 3.696A  pdb=" N   VAL D  71 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 117
      removed outlier: 3.771A  pdb=" N   PHE D  94 " --> pdb=" O   SER D  90 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE D  99 " --> pdb=" O   TYR D  95 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU D 102 " --> pdb=" O   LEU D  98 " (cutoff:3.500A)
      Proline residue:  D 112  - end of helix
    Processing helix  chain 'D' and resid 123 through 145
      removed outlier: 3.880A  pdb=" N   LEU D 141 " --> pdb=" O   PHE D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 172
      removed outlier: 3.505A  pdb=" N   THR D 166 " --> pdb=" O   ARG D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 173 through 181
      removed outlier: 3.725A  pdb=" N   ILE D 181 " --> pdb=" O   LEU D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 191
      removed outlier: 4.044A  pdb=" N   ILE D 186 " --> pdb=" O   PRO D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 218
    Processing helix  chain 'D' and resid 219 through 222
      removed outlier: 3.615A  pdb=" N   LEU D 222 " --> pdb=" O   LEU D 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 219 through 222'
    Processing helix  chain 'D' and resid 223 through 238
      removed outlier: 3.702A  pdb=" N   ARG D 229 " --> pdb=" O   SER D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 276
      removed outlier: 3.720A  pdb=" N   VAL D 249 " --> pdb=" O   ALA D 245 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   CYS D 267 " --> pdb=" O   HIS D 263 " (cutoff:3.500A)
      Proline residue:  D 273  - end of helix
      removed outlier: 3.897A  pdb=" N   GLN D 276 " --> pdb=" O   VAL D 272 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 282 through 287
    Processing helix  chain 'D' and resid 293 through 310
    Processing helix  chain 'D' and resid 321 through 351
      removed outlier: 3.602A  pdb=" N   TRP D 326 " --> pdb=" O   MET D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 352 through 354
      No H-bonds generated for 'chain 'D' and resid 352 through 354'
    Processing helix  chain 'D' and resid 355 through 375
      removed outlier: 3.915A  pdb=" N   TYR D 360 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLN D 361 " --> pdb=" O   ARG D 357 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   HIS D 374 " --> pdb=" O   TYR D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 377 through 393
    Processing helix  chain 'D' and resid 398 through 406
      removed outlier: 3.537A  pdb=" N   LEU D 403 " --> pdb=" O   GLU D 399 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU D 406 " --> pdb=" O   ILE D 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 407 through 419
    Processing helix  chain 'D' and resid 434 through 443
    Processing helix  chain 'D' and resid 518 through 528
      removed outlier: 3.763A  pdb=" N   PHE D 522 " --> pdb=" O   SER D 518 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 445 through 448
    Processing sheet with id=AA2, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 448
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 448
    Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 474

    840 hydrogen bonds defined for protein.
    2484 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: 2.09

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 2036
        1.27 -     1.41: 3966
        1.41 -     1.56: 7818
        1.56 -     1.70: 8
        1.70 -     1.85: 164
  Bond restraints: 13992
  Sorted by residual:
  bond pdb=" CAT VXI D 801 "
       pdb=" CAU VXI D 801 "
    ideal  model  delta    sigma   weight residual
    1.394  1.787 -0.393 2.00e-02 2.50e+03 3.86e+02
  bond pdb=" CAT VXI A 801 "
       pdb=" CAU VXI A 801 "
    ideal  model  delta    sigma   weight residual
    1.394  1.787 -0.393 2.00e-02 2.50e+03 3.86e+02
  bond pdb=" CAT VXI B 801 "
       pdb=" CAU VXI B 801 "
    ideal  model  delta    sigma   weight residual
    1.394  1.787 -0.393 2.00e-02 2.50e+03 3.86e+02
  bond pdb=" CAT VXI C 801 "
       pdb=" CAU VXI C 801 "
    ideal  model  delta    sigma   weight residual
    1.394  1.787 -0.393 2.00e-02 2.50e+03 3.86e+02
  bond pdb=" CAR VXI C 801 "
       pdb=" CAT VXI C 801 "
    ideal  model  delta    sigma   weight residual
    1.512  1.845 -0.333 2.00e-02 2.50e+03 2.77e+02
  ... (remaining 13987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 18375
        2.19 -     4.38: 501
        4.38 -     6.57: 84
        6.57 -     8.75: 52
        8.75 -    10.94: 24
  Bond angle restraints: 19036
  Sorted by residual:
  angle pdb=" C   LEU D 517 "
        pdb=" N   SER D 518 "
        pdb=" CA  SER D 518 "
      ideal   model   delta    sigma   weight residual
     121.31  128.22   -6.91 1.49e+00 4.50e-01 2.15e+01
  angle pdb=" C   LEU C 517 "
        pdb=" N   SER C 518 "
        pdb=" CA  SER C 518 "
      ideal   model   delta    sigma   weight residual
     121.31  128.19   -6.88 1.49e+00 4.50e-01 2.13e+01
  angle pdb=" C   LEU A 517 "
        pdb=" N   SER A 518 "
        pdb=" CA  SER A 518 "
      ideal   model   delta    sigma   weight residual
     121.31  128.19   -6.88 1.49e+00 4.50e-01 2.13e+01
  angle pdb=" C   LEU B 517 "
        pdb=" N   SER B 518 "
        pdb=" CA  SER B 518 "
      ideal   model   delta    sigma   weight residual
     121.31  128.19   -6.88 1.49e+00 4.50e-01 2.13e+01
  angle pdb=" C   VAL B 455 "
        pdb=" N   VAL B 456 "
        pdb=" CA  VAL B 456 "
      ideal   model   delta    sigma   weight residual
     121.97  130.08   -8.11 1.80e+00 3.09e-01 2.03e+01
  ... (remaining 19031 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.77: 7730
       14.77 -    29.54: 330
       29.54 -    44.30: 44
       44.30 -    59.07: 12
       59.07 -    73.84: 16
  Dihedral angle restraints: 8132
    sinusoidal: 3076
      harmonic: 5056
  Sorted by residual:
  dihedral pdb=" CA  VAL B 455 "
           pdb=" C   VAL B 455 "
           pdb=" N   VAL B 456 "
           pdb=" CA  VAL B 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.73   44.27     0      5.00e+00 4.00e-02 7.84e+01
  dihedral pdb=" CA  VAL A 455 "
           pdb=" C   VAL A 455 "
           pdb=" N   VAL A 456 "
           pdb=" CA  VAL A 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.73   44.27     0      5.00e+00 4.00e-02 7.84e+01
  dihedral pdb=" CA  VAL C 455 "
           pdb=" C   VAL C 455 "
           pdb=" N   VAL C 456 "
           pdb=" CA  VAL C 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.73   44.27     0      5.00e+00 4.00e-02 7.84e+01
  ... (remaining 8129 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1250
       0.039 -    0.079: 667
       0.079 -    0.118: 187
       0.118 -    0.157: 17
       0.157 -    0.196: 35
  Chirality restraints: 2156
  Sorted by residual:
  chirality pdb=" CG  LEU D 410 "
            pdb=" CB  LEU D 410 "
            pdb=" CD1 LEU D 410 "
            pdb=" CD2 LEU D 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality pdb=" CG  LEU A 410 "
            pdb=" CB  LEU A 410 "
            pdb=" CD1 LEU A 410 "
            pdb=" CD2 LEU A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" CG  LEU B 410 "
            pdb=" CB  LEU B 410 "
            pdb=" CD1 LEU B 410 "
            pdb=" CD2 LEU B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.20 2.00e-01 2.50e+01 9.51e-01
  ... (remaining 2153 not shown)

  Planarity restraints: 2340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 455 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   VAL D 455 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL D 455 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL D 456 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 455 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.66e+00
        pdb=" C   VAL A 455 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   VAL A 455 "    0.017 2.00e-02 2.50e+03
        pdb=" N   VAL A 456 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 455 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.66e+00
        pdb=" C   VAL C 455 "    0.045 2.00e-02 2.50e+03
        pdb=" O   VAL C 455 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   VAL C 456 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2337 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 4610
        2.88 -     3.38: 12743
        3.38 -     3.89: 21519
        3.89 -     4.39: 22667
        4.39 -     4.90: 40154
  Nonbonded interactions: 101693
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 359 "
            pdb=" NE2 GLN D 366 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OE1 GLN C 359 "
            pdb=" NE2 GLN A 366 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" OE1 GLN A 359 "
            pdb=" NE2 GLN B 366 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" NE2 GLN C 366 "
            pdb=" OE1 GLN D 359 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" OE2 GLU C 458 "
            pdb=" N   SER C 505 "
     model   vdw
     2.415 3.120
  ... (remaining 101688 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     12.260
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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      :  0.015   0.393  13992  Z= 0.726
  Angle     :  1.000  10.942  19036  Z= 0.535
  Chirality :  0.052   0.196   2156
  Planarity :  0.006   0.044   2340
  Dihedral  :  9.714  73.839   4852
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  0.58 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -2.78 (0.16), residues: 1672
  helix: -1.33 (0.12), residues: 1128
  sheet: -0.61 (0.67), residues: 72
  loop : -3.00 (0.23), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 229 
 TYR   0.028   0.002   TYR D 511 
 PHE   0.015   0.002   PHE D 449 
 TRP   0.031   0.002   TRP A 234 
 HIS   0.015   0.003   HIS B 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.01470 (13992)
  covalent geometry    : angle       0.99961 (19036)
  hydrogen bonds       : bond        0.15619 (  840)
  hydrogen bonds       : angle       6.04194 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.503 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9378 (m-40) cc_final: 0.9175 (m-40)
REVERT: A  523 ASN cc_start: 0.9377 (m-40) cc_final: 0.9173 (m-40)
REVERT: B  523 ASN cc_start: 0.9377 (m-40) cc_final: 0.9176 (m-40)
REVERT: D  523 ASN cc_start: 0.9388 (m-40) cc_final: 0.9182 (m-40)
  outliers start: 8
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1376
  time to fit residues: 25.4401
Evaluate side-chains
  87 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  456 VAL
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain D residue  455 VAL
Chi-restraints excluded: chain D residue  456 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    2.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 107 ASN
C 292 HIS
C 300 HIS
C 308 HIS
C 470 HIS
A 107 ASN
A 292 HIS
A 300 HIS
A 308 HIS
A 470 HIS
B 107 ASN
B 292 HIS
B 300 HIS
B 308 HIS
B 470 HIS
D 292 HIS
D 300 HIS
D 308 HIS
D 470 HIS

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.068805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.052384 restraints weight = 57405.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 3.36
r_work: 0.2906 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13992  Z= 0.174
  Angle     :  0.585   6.911  19036  Z= 0.310
  Chirality :  0.042   0.120   2156
  Planarity :  0.004   0.040   2340
  Dihedral  :  6.802  56.859   2004
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  2.77 %
    Favored  : 95.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  0.35 (0.20), residues: 1672
  helix:  1.17 (0.15), residues: 1148
  sheet:  0.80 (0.64), residues: 72
  loop : -2.36 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 223 
 TYR   0.015   0.002   TYR B 511 
 PHE   0.011   0.001   PHE D 467 
 TRP   0.014   0.001   TRP D 234 
 HIS   0.006   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (13992)
  covalent geometry    : angle       0.58525 (19036)
  hydrogen bonds       : bond        0.05449 (  840)
  hydrogen bonds       : angle       4.16858 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.547 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9398 (m-40) cc_final: 0.9192 (m-40)
REVERT: A  523 ASN cc_start: 0.9400 (m-40) cc_final: 0.9193 (m-40)
REVERT: B  523 ASN cc_start: 0.9399 (m-40) cc_final: 0.9193 (m-40)
REVERT: D  523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9194 (m-40)
  outliers start: 18
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0916
  time to fit residues: 15.3575
Evaluate side-chains
  95 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  456 VAL
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain B residue  144 ASN
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain D residue  425 HIS
Chi-restraints excluded: chain D residue  455 VAL
Chi-restraints excluded: chain D residue  456 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0170
   chunk 119 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 171 optimal weight:   20.0000
   chunk 137 optimal weight:    3.9990
   chunk 78 optimal weight:   30.0000
   chunk 117 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   overall best weight:    4.6026

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.068877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.052419 restraints weight = 57691.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 3.37
r_work: 0.2901 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13992  Z= 0.148
  Angle     :  0.529   6.757  19036  Z= 0.276
  Chirality :  0.041   0.119   2156
  Planarity :  0.003   0.040   2340
  Dihedral  :  6.335  55.780   2004
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  3.28 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.21), residues: 1672
  helix:  2.11 (0.16), residues: 1152
  sheet:  1.50 (0.67), residues: 72
  loop : -1.93 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 226 
 TYR   0.016   0.001   TYR B 511 
 PHE   0.011   0.001   PHE B 417 
 TRP   0.009   0.001   TRP A 326 
 HIS   0.005   0.001   HIS B 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13992)
  covalent geometry    : angle       0.52873 (19036)
  hydrogen bonds       : bond        0.04757 (  840)
  hydrogen bonds       : angle       3.79884 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.442 
Fit side-chains
REVERT: C  309 MET cc_start: 0.9266 (mmm) cc_final: 0.9048 (mmm)
REVERT: C  523 ASN cc_start: 0.9394 (m-40) cc_final: 0.9184 (m-40)
REVERT: A  309 MET cc_start: 0.9270 (mmm) cc_final: 0.9053 (mmm)
REVERT: A  523 ASN cc_start: 0.9395 (m-40) cc_final: 0.9186 (m-40)
REVERT: B  309 MET cc_start: 0.9278 (mmm) cc_final: 0.9062 (mmm)
REVERT: B  523 ASN cc_start: 0.9397 (m-40) cc_final: 0.9189 (m-40)
REVERT: D  309 MET cc_start: 0.9265 (mmm) cc_final: 0.9050 (mmm)
REVERT: D  523 ASN cc_start: 0.9393 (m-40) cc_final: 0.9183 (m-40)
  outliers start: 23
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0960
  time to fit residues: 15.4249
Evaluate side-chains
  88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  456 VAL
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain D residue  425 HIS
Chi-restraints excluded: chain D residue  455 VAL
Chi-restraints excluded: chain D residue  456 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 10 optimal weight:    0.0370
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    9.9990
   chunk 130 optimal weight:    8.9990
   chunk 111 optimal weight:    8.9990
   chunk 51 optimal weight:    0.1980
   chunk 161 optimal weight:    6.9990
   chunk 157 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 41 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0570
   overall best weight:    2.0580

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.070651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.054069 restraints weight = 57315.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.40
r_work: 0.2940 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  13992  Z= 0.097
  Angle     :  0.466   6.547  19036  Z= 0.244
  Chirality :  0.039   0.117   2156
  Planarity :  0.003   0.041   2340
  Dihedral  :  6.206  58.682   2004
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  4.52 %
    Favored  : 94.02 %
  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:  2.14 (0.22), residues: 1672
  helix:  2.49 (0.16), residues: 1152
  sheet:  1.25 (0.82), residues: 52
  loop : -1.44 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 226 
 TYR   0.012   0.001   TYR D 511 
 PHE   0.009   0.001   PHE D 270 
 TRP   0.008   0.001   TRP D 326 
 HIS   0.003   0.001   HIS C 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 (13992)
  covalent geometry    : angle       0.46602 (19036)
  hydrogen bonds       : bond        0.03724 (  840)
  hydrogen bonds       : angle       3.55358 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.470 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9197 (m110)
REVERT: A  523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9199 (m110)
REVERT: B  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9201 (m110)
REVERT: D  523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9191 (m-40)
  outliers start: 20
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0839
  time to fit residues: 13.5110
Evaluate side-chains
  92 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain C residue  455 VAL
Chi-restraints excluded: chain C residue  456 VAL
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain B residue  455 VAL
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Chi-restraints excluded: chain D residue  455 VAL
Chi-restraints excluded: chain D residue  456 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 86 optimal weight:   30.0000
   chunk 134 optimal weight:    9.9990
   chunk 155 optimal weight:    0.9990
   chunk 150 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 129 optimal weight:   30.0000
   chunk 41 optimal weight:   20.0000
   chunk 93 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 253 ASN
A 253 ASN
B 253 ASN
D 253 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.069333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.052634 restraints weight = 57345.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 3.37
r_work: 0.2903 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13992  Z= 0.126
  Angle     :  0.492   6.566  19036  Z= 0.256
  Chirality :  0.040   0.129   2156
  Planarity :  0.003   0.042   2340
  Dihedral  :  6.189  57.942   2004
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  5.47 %
    Favored  : 93.37 %
  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:  2.45 (0.22), residues: 1672
  helix:  2.68 (0.16), residues: 1156
  sheet:  1.31 (0.66), residues: 72
  loop : -1.37 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 226 
 TYR   0.013   0.001   TYR C 511 
 PHE   0.010   0.001   PHE D 270 
 TRP   0.008   0.001   TRP A 326 
 HIS   0.004   0.001   HIS D 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13992)
  covalent geometry    : angle       0.49242 (19036)
  hydrogen bonds       : bond        0.04359 (  840)
  hydrogen bonds       : angle       3.54320 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.551 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9404 (m-40) cc_final: 0.9189 (m110)
REVERT: A  523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9191 (m110)
REVERT: B  523 ASN cc_start: 0.9408 (m-40) cc_final: 0.9195 (m110)
REVERT: D  523 ASN cc_start: 0.9410 (m-40) cc_final: 0.9201 (m110)
  outliers start: 16
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0827
  time to fit residues: 12.7326
Evaluate side-chains
  88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain C residue  456 VAL
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Chi-restraints excluded: chain D residue  456 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 143 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 150 optimal weight:    0.2980
   chunk 50 optimal weight:    6.9990
   chunk 108 optimal weight:    0.0270
   chunk 149 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 69 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   overall best weight:    1.6442

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

Flipped N/Q/H residues before XYZ refinement:
C 269 GLN
A 269 GLN
B 269 GLN
D 269 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.071026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.054611 restraints weight = 56789.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 3.36
r_work: 0.2953 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  13992  Z= 0.090
  Angle     :  0.458   6.438  19036  Z= 0.240
  Chirality :  0.039   0.116   2156
  Planarity :  0.003   0.043   2340
  Dihedral  :  5.996  57.982   2000
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  5.25 %
    Favored  : 93.88 %
  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:  2.62 (0.22), residues: 1672
  helix:  2.79 (0.15), residues: 1156
  sheet:  1.25 (0.82), residues: 52
  loop : -1.09 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.010   0.001   TYR A 511 
 PHE   0.009   0.001   PHE B 270 
 TRP   0.007   0.001   TRP D 326 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 (13992)
  covalent geometry    : angle       0.45828 (19036)
  hydrogen bonds       : bond        0.03429 (  840)
  hydrogen bonds       : angle       3.39189 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.536 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9191 (m110)
REVERT: A  523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9192 (m110)
REVERT: B  523 ASN cc_start: 0.9409 (m-40) cc_final: 0.9197 (m110)
REVERT: D  523 ASN cc_start: 0.9411 (m-40) cc_final: 0.9192 (m110)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 0.0919
  time to fit residues: 13.5738
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 35 optimal weight:   30.0000
   chunk 146 optimal weight:   10.0000
   chunk 78 optimal weight:   30.0000
   chunk 70 optimal weight:    9.9990
   chunk 126 optimal weight:   50.0000
   chunk 76 optimal weight:   20.0000
   chunk 140 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 26 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    4.7588

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.068767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052064 restraints weight = 57129.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 3.34
r_work: 0.2891 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13992  Z= 0.147
  Angle     :  0.504   6.541  19036  Z= 0.264
  Chirality :  0.041   0.171   2156
  Planarity :  0.003   0.042   2340
  Dihedral  :  5.933  59.121   1996
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.69 %
    Favored  : 93.73 %
  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:  2.74 (0.22), residues: 1672
  helix:  2.83 (0.16), residues: 1160
  sheet:  1.41 (0.67), residues: 72
  loop : -1.07 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.013   0.001   TYR A 511 
 PHE   0.009   0.001   PHE D 270 
 TRP   0.009   0.001   TRP D 234 
 HIS   0.004   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13992)
  covalent geometry    : angle       0.50443 (19036)
  hydrogen bonds       : bond        0.04537 (  840)
  hydrogen bonds       : angle       3.48228 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.585 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9404 (m-40) cc_final: 0.9183 (m110)
REVERT: A  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9187 (m110)
REVERT: B  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9188 (m110)
REVERT: D  523 ASN cc_start: 0.9412 (m-40) cc_final: 0.9186 (m110)
  outliers start: 8
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0981
  time to fit residues: 13.5710
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 168 optimal weight:   20.0000
   chunk 20 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 162 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 119 optimal weight:   20.0000
   chunk 146 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.068425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.051725 restraints weight = 56771.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 3.34
r_work: 0.2882 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13992  Z= 0.151
  Angle     :  0.513   6.533  19036  Z= 0.268
  Chirality :  0.041   0.137   2156
  Planarity :  0.003   0.043   2340
  Dihedral  :  5.941  57.177   1996
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  5.03 %
    Favored  : 94.10 %
  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:  2.81 (0.22), residues: 1672
  helix:  2.84 (0.15), residues: 1160
  sheet:  1.58 (0.83), residues: 52
  loop : -0.80 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.014   0.001   TYR C 511 
 PHE   0.009   0.001   PHE A 270 
 TRP   0.009   0.001   TRP C 234 
 HIS   0.004   0.001   HIS C 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (13992)
  covalent geometry    : angle       0.51294 (19036)
  hydrogen bonds       : bond        0.04646 (  840)
  hydrogen bonds       : angle       3.51277 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.556 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9404 (m-40) cc_final: 0.9176 (m110)
REVERT: A  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9180 (m110)
REVERT: B  523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9179 (m110)
REVERT: D  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9176 (m110)
  outliers start: 12
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0809
  time to fit residues: 11.7904
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 80 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 118 optimal weight:    9.9990
   chunk 141 optimal weight:    1.9990
   chunk 36 optimal weight:   30.0000
   chunk 68 optimal weight:    1.9990
   chunk 120 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 148 optimal weight:    3.9990
   chunk 155 optimal weight:    6.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.068906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.052173 restraints weight = 57378.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 3.38
r_work: 0.2900 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13992  Z= 0.126
  Angle     :  0.497   6.472  19036  Z= 0.258
  Chirality :  0.040   0.131   2156
  Planarity :  0.003   0.043   2340
  Dihedral  :  5.775  54.718   1996
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.03 %
    Favored  : 94.39 %
  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:  2.89 (0.22), residues: 1672
  helix:  2.92 (0.15), residues: 1160
  sheet:  1.31 (0.64), residues: 72
  loop : -0.91 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 226 
 TYR   0.013   0.001   TYR A 511 
 PHE   0.010   0.001   PHE C 467 
 TRP   0.008   0.001   TRP B 234 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (13992)
  covalent geometry    : angle       0.49661 (19036)
  hydrogen bonds       : bond        0.04289 (  840)
  hydrogen bonds       : angle       3.46641 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.460 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9400 (m-40) cc_final: 0.9167 (m110)
REVERT: A  523 ASN cc_start: 0.9401 (m-40) cc_final: 0.9170 (m110)
REVERT: B  523 ASN cc_start: 0.9403 (m-40) cc_final: 0.9173 (m110)
REVERT: D  523 ASN cc_start: 0.9405 (m-40) cc_final: 0.9174 (m110)
  outliers start: 8
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0829
  time to fit residues: 11.3400
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 149 optimal weight:    0.9990
   chunk 82 optimal weight:   30.0000
   chunk 127 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 136 optimal weight:   30.0000
   chunk 90 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 169 optimal weight:   50.0000
   overall best weight:    4.1388

-------------------------------------------------------------------------------
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 = 0.3550 r_free = 0.3550 target = 0.068841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.052073 restraints weight = 57426.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 3.36
r_work: 0.2896 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13992  Z= 0.136
  Angle     :  0.518   6.731  19036  Z= 0.269
  Chirality :  0.041   0.178   2156
  Planarity :  0.003   0.043   2340
  Dihedral  :  5.786  54.249   1996
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.47 %
    Favored  : 93.95 %
  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:  2.88 (0.22), residues: 1672
  helix:  2.89 (0.15), residues: 1160
  sheet:  1.26 (0.80), residues: 52
  loop : -0.72 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 226 
 TYR   0.013   0.001   TYR C 511 
 PHE   0.011   0.001   PHE D 467 
 TRP   0.010   0.001   TRP B 234 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (13992)
  covalent geometry    : angle       0.51793 (19036)
  hydrogen bonds       : bond        0.04445 (  840)
  hydrogen bonds       : angle       3.49407 ( 2484)

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

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

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3344 Ramachandran restraints generated.
    1672 Oldfield, 0 Emsley, 1672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.554 
Fit side-chains
REVERT: C  523 ASN cc_start: 0.9406 (m-40) cc_final: 0.9174 (m110)
REVERT: A  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9175 (m110)
REVERT: B  523 ASN cc_start: 0.9407 (m-40) cc_final: 0.9176 (m110)
REVERT: D  523 ASN cc_start: 0.9401 (m-40) cc_final: 0.9167 (m110)
  outliers start: 8
  outliers final: 8
  residues processed: 84
  average time/residue: 0.0871
  time to fit residues: 12.2115
Evaluate side-chains
  84 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  145 PHE
Chi-restraints excluded: chain C residue  425 HIS
Chi-restraints excluded: chain A residue  145 PHE
Chi-restraints excluded: chain A residue  425 HIS
Chi-restraints excluded: chain B residue  145 PHE
Chi-restraints excluded: chain B residue  425 HIS
Chi-restraints excluded: chain D residue  145 PHE
Chi-restraints excluded: chain D residue  425 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 166 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 87 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 152 optimal weight:    3.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.069192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.052600 restraints weight = 57301.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 3.36
r_work: 0.2914 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13992  Z= 0.121
  Angle     :  0.510   8.246  19036  Z= 0.264
  Chirality :  0.040   0.202   2156
  Planarity :  0.003   0.043   2340
  Dihedral  :  5.703  55.578   1996
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.69 %
    Favored  : 93.73 %
  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:  2.84 (0.22), residues: 1672
  helix:  2.87 (0.15), residues: 1160
  sheet:  1.80 (0.78), residues: 48
  loop : -0.82 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.012   0.001   TYR C 511 
 PHE   0.012   0.001   PHE C 467 
 TRP   0.020   0.001   TRP B  96 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13992)
  covalent geometry    : angle       0.50965 (19036)
  hydrogen bonds       : bond        0.04265 (  840)
  hydrogen bonds       : angle       3.47716 ( 2484)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3575.68 seconds
wall clock time: 61 minutes 50.84 seconds (3710.84 seconds total)