Starting phenix.real_space_refine
on Fri Aug 22 20:34:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gw7_34304/08_2025/8gw7_34304.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.027
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
     S      39      5.16       5
     Cl      6      4.86       5
     C    5169      2.51       5
     N    1128      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 7524
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2471
          Classifications: {'peptide': 315}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 20, 'TRANS': 294}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 38
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 37
          Unusual residues: {' CL': 2, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 1.73, per 1000 atoms: 0.23
  Number of scatterers: 7524
  At special positions: 0
  Unit cell: (106.68, 97.44, 66.36, 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)
     Cl      6     17.00
     S      39     16.00
     O    1182      8.00
     N    1128      7.00
     C    5169      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: 0.45
  Conformation dependent library (CDL) restraints added in 276.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1806

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      81.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 189 through 191
      No H-bonds generated for 'chain 'A' and resid 189 through 191'
    Processing helix  chain 'A' and resid 192 through 212
      removed outlier: 4.310A  pdb=" N   CYS A 196 " --> pdb=" O   CYS A 192 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 219
      removed outlier: 3.752A  pdb=" N   LEU A 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 250
      removed outlier: 3.842A  pdb=" N   LEU A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 260
      removed outlier: 3.757A  pdb=" N   PHE A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   HIS A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 267
      removed outlier: 3.526A  pdb=" N   VAL A 264 " --> pdb=" O   PRO A 261 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASN A 265 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE A 266 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 281
      removed outlier: 3.743A  pdb=" N   CYS A 274 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   MET A 275 " --> pdb=" O   TRP A 271 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER A 280 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 318
      removed outlier: 4.377A  pdb=" N   TRP A 297 " --> pdb=" O   HIS A 293 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A 298 " --> pdb=" O   PRO A 294 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE A 300 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      Proline residue:  A 303  - end of helix
      removed outlier: 3.687A  pdb=" N   TRP A 315 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 316 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 349
      removed outlier: 3.892A  pdb=" N   PHE A 339 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A 343 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 375
      removed outlier: 4.079A  pdb=" N   VAL A 367 " --> pdb=" O   ALA A 363 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG A 375 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 392
      removed outlier: 3.666A  pdb=" N   SER A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   MET A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 409
    Processing helix  chain 'A' and resid 412 through 433
      removed outlier: 3.622A  pdb=" N   LEU A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 466
      removed outlier: 3.916A  pdb=" N   TYR A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 449 " --> pdb=" O   TRP A 445 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE A 450 " --> pdb=" O   TRP A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.548A  pdb=" N   LYS A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 499
      removed outlier: 3.842A  pdb=" N   ALA A 497 " --> pdb=" O   THR A 493 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 499 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 189 through 191
      No H-bonds generated for 'chain 'C' and resid 189 through 191'
    Processing helix  chain 'C' and resid 192 through 212
      removed outlier: 4.309A  pdb=" N   CYS C 196 " --> pdb=" O   CYS C 192 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA C 203 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL C 204 " --> pdb=" O   SER C 200 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU C 205 " --> pdb=" O   SER C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 219
      removed outlier: 3.752A  pdb=" N   LEU C 218 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 250
      removed outlier: 3.843A  pdb=" N   LEU C 226 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 260
      removed outlier: 3.756A  pdb=" N   PHE C 259 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   HIS C 260 " --> pdb=" O   ARG C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 267
      removed outlier: 3.527A  pdb=" N   VAL C 264 " --> pdb=" O   PRO C 261 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASN C 265 " --> pdb=" O   VAL C 262 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   PHE C 266 " --> pdb=" O   ARG C 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 281
      removed outlier: 3.744A  pdb=" N   CYS C 274 " --> pdb=" O   PRO C 270 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   MET C 275 " --> pdb=" O   TRP C 271 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE C 276 " --> pdb=" O   VAL C 272 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER C 280 " --> pdb=" O   PHE C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 318
      removed outlier: 4.377A  pdb=" N   TRP C 297 " --> pdb=" O   HIS C 293 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS C 298 " --> pdb=" O   PRO C 294 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE C 300 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
      removed outlier: 3.687A  pdb=" N   TRP C 315 " --> pdb=" O   ILE C 311 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU C 316 " --> pdb=" O   TYR C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 349
      removed outlier: 3.892A  pdb=" N   PHE C 339 " --> pdb=" O   VAL C 335 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE C 343 " --> pdb=" O   PHE C 339 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 375
      removed outlier: 4.079A  pdb=" N   VAL C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG C 375 " --> pdb=" O   THR C 371 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 392
      removed outlier: 3.666A  pdb=" N   SER C 391 " --> pdb=" O   HIS C 387 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   MET C 392 " --> pdb=" O   PRO C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 409
    Processing helix  chain 'C' and resid 412 through 433
      removed outlier: 3.622A  pdb=" N   LEU C 429 " --> pdb=" O   LEU C 425 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL C 430 " --> pdb=" O   TYR C 426 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 444 through 466
      removed outlier: 3.916A  pdb=" N   TYR C 448 " --> pdb=" O   ALA C 444 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   THR C 449 " --> pdb=" O   TRP C 445 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   PHE C 450 " --> pdb=" O   TRP C 446 " (cutoff:3.500A)
      Proline residue:  C 451  - end of helix
      removed outlier: 3.548A  pdb=" N   LYS C 461 " --> pdb=" O   VAL C 457 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 468 through 499
      removed outlier: 3.842A  pdb=" N   ALA C 497 " --> pdb=" O   THR C 493 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE C 498 " --> pdb=" O   LEU C 494 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL C 499 " --> pdb=" O   LEU C 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 191
      No H-bonds generated for 'chain 'B' and resid 189 through 191'
    Processing helix  chain 'B' and resid 192 through 212
      removed outlier: 4.310A  pdb=" N   CYS B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL B 204 " --> pdb=" O   SER B 200 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B 205 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 219
      removed outlier: 3.752A  pdb=" N   LEU B 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
      removed outlier: 3.842A  pdb=" N   LEU B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 260
      removed outlier: 3.757A  pdb=" N   PHE B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   HIS B 260 " --> pdb=" O   ARG B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 267
      removed outlier: 3.525A  pdb=" N   VAL B 264 " --> pdb=" O   PRO B 261 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ASN B 265 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   PHE B 266 " --> pdb=" O   ARG B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 281
      removed outlier: 3.744A  pdb=" N   CYS B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   MET B 275 " --> pdb=" O   TRP B 271 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER B 280 " --> pdb=" O   PHE B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 318
      removed outlier: 4.377A  pdb=" N   TRP B 297 " --> pdb=" O   HIS B 293 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS B 298 " --> pdb=" O   PRO B 294 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B 300 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
      removed outlier: 3.687A  pdb=" N   TRP B 315 " --> pdb=" O   ILE B 311 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU B 316 " --> pdb=" O   TYR B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 349
      removed outlier: 3.893A  pdb=" N   PHE B 339 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B 343 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 375
      removed outlier: 4.079A  pdb=" N   VAL B 367 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B 375 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 392
      removed outlier: 3.667A  pdb=" N   SER B 391 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   MET B 392 " --> pdb=" O   PRO B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 409
    Processing helix  chain 'B' and resid 412 through 433
      removed outlier: 3.623A  pdb=" N   LEU B 429 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   VAL B 430 " --> pdb=" O   TYR B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 466
      removed outlier: 3.915A  pdb=" N   TYR B 448 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR B 449 " --> pdb=" O   TRP B 445 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE B 450 " --> pdb=" O   TRP B 446 " (cutoff:3.500A)
      Proline residue:  B 451  - end of helix
      removed outlier: 3.547A  pdb=" N   LYS B 461 " --> pdb=" O   VAL B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 499
      removed outlier: 3.841A  pdb=" N   ALA B 497 " --> pdb=" O   THR B 493 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   PHE B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL B 499 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)

    474 hydrogen bonds defined for protein.
    1404 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: 0.96

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1185
        1.33 -     1.45: 2368
        1.45 -     1.57: 4211
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 7818
  Sorted by residual:
  bond pdb=" CBD Y01 B 903 "
       pdb=" CBF Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.536  1.463  0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" CBD Y01 C 903 "
       pdb=" CBF Y01 C 903 "
    ideal  model  delta    sigma   weight residual
    1.536  1.463  0.073 2.00e-02 2.50e+03 1.34e+01
  bond pdb=" CBD Y01 A 903 "
       pdb=" CBF Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.536  1.463  0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" CAK Y01 A 903 "
       pdb=" CBD Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.525  1.467  0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" CAK Y01 B 903 "
       pdb=" CBD Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.525  1.467  0.058 2.00e-02 2.50e+03 8.45e+00
  ... (remaining 7813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10564
        2.36 -     4.73: 119
        4.73 -     7.09: 39
        7.09 -     9.45: 13
        9.45 -    11.81: 14
  Bond angle restraints: 10749
  Sorted by residual:
  angle pdb=" CAK Y01 A 903 "
        pdb=" CAI Y01 A 903 "
        pdb=" CAZ Y01 A 903 "
      ideal   model   delta    sigma   weight residual
     124.96  113.15   11.81 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CAK Y01 C 903 "
        pdb=" CAI Y01 C 903 "
        pdb=" CAZ Y01 C 903 "
      ideal   model   delta    sigma   weight residual
     124.96  113.21   11.75 3.00e+00 1.11e-01 1.53e+01
  angle pdb=" CAK Y01 B 903 "
        pdb=" CAI Y01 B 903 "
        pdb=" CAZ Y01 B 903 "
      ideal   model   delta    sigma   weight residual
     124.96  113.25   11.71 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CAD Y01 A 903 "
        pdb=" CBH Y01 A 903 "
        pdb=" CAZ Y01 A 903 "
      ideal   model   delta    sigma   weight residual
     108.53   98.20   10.33 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" CAD Y01 B 903 "
        pdb=" CBH Y01 B 903 "
        pdb=" CAZ Y01 B 903 "
      ideal   model   delta    sigma   weight residual
     108.53   98.23   10.30 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 10744 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 4030
       17.05 -    34.10: 350
       34.10 -    51.16: 87
       51.16 -    68.21: 15
       68.21 -    85.26: 6
  Dihedral angle restraints: 4488
    sinusoidal: 1701
      harmonic: 2787
  Sorted by residual:
  dihedral pdb=" CB  GLU C 308 "
           pdb=" CG  GLU C 308 "
           pdb=" CD  GLU C 308 "
           pdb=" OE1 GLU C 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.26   85.26     1      3.00e+01 1.11e-03 9.79e+00
  dihedral pdb=" CB  GLU B 308 "
           pdb=" CG  GLU B 308 "
           pdb=" CD  GLU B 308 "
           pdb=" OE1 GLU B 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.26   85.26     1      3.00e+01 1.11e-03 9.79e+00
  dihedral pdb=" CB  GLU A 308 "
           pdb=" CG  GLU A 308 "
           pdb=" CD  GLU A 308 "
           pdb=" OE1 GLU A 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.24   85.24     1      3.00e+01 1.11e-03 9.78e+00
  ... (remaining 4485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 1212
       0.144 -    0.288: 6
       0.288 -    0.431: 9
       0.431 -    0.575: 0
       0.575 -    0.719: 3
  Chirality restraints: 1230
  Sorted by residual:
  chirality pdb=" CBH Y01 A 903 "
            pdb=" CAT Y01 A 903 "
            pdb=" CAZ Y01 A 903 "
            pdb=" CBF Y01 A 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.13   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CBH Y01 B 903 "
            pdb=" CAT Y01 B 903 "
            pdb=" CAZ Y01 B 903 "
            pdb=" CBF Y01 B 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.13   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CBH Y01 C 903 "
            pdb=" CAT Y01 C 903 "
            pdb=" CAZ Y01 C 903 "
            pdb=" CBF Y01 C 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.14   -0.72 2.00e-01 2.50e+01 1.28e+01
  ... (remaining 1227 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 286 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO B 287 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 287 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 287 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 286 "    0.036 5.00e-02 4.00e+02   5.50e-02 4.84e+00
        pdb=" N   PRO A 287 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 286 "   -0.036 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO C 287 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C 287 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 287 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 970
        2.76 -     3.29: 7878
        3.29 -     3.83: 11781
        3.83 -     4.36: 13144
        4.36 -     4.90: 22551
  Nonbonded interactions: 56324
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 202 "
            pdb=" OG1 THR B 453 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OE1 GLN A 202 "
            pdb=" OG1 THR A 453 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OE1 GLN C 202 "
            pdb=" OG1 THR C 453 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   PHE A 498 "
            pdb=" NE2 GLN A 501 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   PHE C 498 "
            pdb=" NE2 GLN C 501 "
     model   vdw
     2.288 3.120
  ... (remaining 56319 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             1.090
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.250
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
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      :  0.004   0.073   7818  Z= 0.190
  Angle     :  0.789  11.813  10749  Z= 0.331
  Chirality :  0.060   0.719   1230
  Planarity :  0.006   0.055   1269
  Dihedral  : 13.998  85.261   2682
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  1.96 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.51 (0.25), residues: 933
  helix:  1.58 (0.18), residues: 651
  sheet:  None (None), residues: 0
  loop : -0.26 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 187 
 TYR   0.012   0.001   TYR B 390 
 PHE   0.006   0.001   PHE A 217 
 TRP   0.008   0.001   TRP B 446 
 HIS   0.004   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 7818)
  covalent geometry    : angle       0.78868 (10749)
  hydrogen bonds       : bond        0.30221 (  474)
  hydrogen bonds       : angle       6.48778 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 185
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  195 ILE cc_start: 0.8634 (tt) cc_final: 0.8266 (pt)
REVERT: A  255 LYS cc_start: 0.8077 (tttm) cc_final: 0.7750 (ttpp)
REVERT: A  469 TYR cc_start: 0.7262 (m-80) cc_final: 0.6965 (m-80)
REVERT: C  195 ILE cc_start: 0.8831 (tt) cc_final: 0.8412 (pt)
REVERT: C  469 TYR cc_start: 0.7321 (m-80) cc_final: 0.7109 (m-80)
REVERT: B  195 ILE cc_start: 0.8778 (tt) cc_final: 0.8445 (pt)
REVERT: B  469 TYR cc_start: 0.7266 (m-80) cc_final: 0.6989 (m-80)
  outliers start: 3
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0684
  time to fit residues: 18.1852
Evaluate side-chains
  149 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 ASN
A 405 ASN
C 219 HIS
C 405 ASN
B 219 HIS
B 405 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.162916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.142701 restraints weight = 12560.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.45
r_work: 0.3611 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7818  Z= 0.167
  Angle     :  0.635   8.857  10749  Z= 0.316
  Chirality :  0.043   0.143   1230
  Planarity :  0.005   0.040   1269
  Dihedral  :  7.653  48.055   1212
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.20 %
    Favored  : 84.97 %
  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:  2.67 (0.28), residues: 933
  helix:  2.40 (0.20), residues: 675
  sheet:  None (None), residues: 0
  loop :  0.07 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 472 
 TYR   0.016   0.002   TYR A 365 
 PHE   0.018   0.001   PHE B 184 
 TRP   0.013   0.001   TRP C 206 
 HIS   0.003   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7818)
  covalent geometry    : angle       0.63489 (10749)
  hydrogen bonds       : bond        0.07581 (  474)
  hydrogen bonds       : angle       4.27620 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  201 SER cc_start: 0.8333 (m) cc_final: 0.8111 (m)
REVERT: A  255 LYS cc_start: 0.8093 (tttm) cc_final: 0.7878 (ttpp)
REVERT: B  255 LYS cc_start: 0.8246 (tttm) cc_final: 0.7739 (mttm)
REVERT: B  375 ARG cc_start: 0.7706 (ptp-170) cc_final: 0.7439 (ptp90)
  outliers start: 14
  outliers final: 12
  residues processed: 173
  average time/residue: 0.0672
  time to fit residues: 16.4212
Evaluate side-chains
  156 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 144
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  368 VAL
Chi-restraints excluded: chain C residue  393 PHE
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 219 HIS
** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 HIS
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.163943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.142354 restraints weight = 12329.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.57
r_work: 0.3613 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7818  Z= 0.131
  Angle     :  0.570   8.286  10749  Z= 0.277
  Chirality :  0.041   0.162   1230
  Planarity :  0.005   0.035   1269
  Dihedral  :  7.298  42.418   1212
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.69 %
    Favored  : 81.57 %
  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:  2.66 (0.28), residues: 933
  helix:  2.46 (0.20), residues: 681
  sheet:  None (None), residues: 0
  loop : -0.21 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 472 
 TYR   0.009   0.001   TYR C 365 
 PHE   0.016   0.001   PHE A 184 
 TRP   0.012   0.001   TRP B 206 
 HIS   0.003   0.001   HIS C 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7818)
  covalent geometry    : angle       0.57005 (10749)
  hydrogen bonds       : bond        0.05342 (  474)
  hydrogen bonds       : angle       3.70634 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 151
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  314 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8234 (tm-30)
REVERT: A  375 ARG cc_start: 0.7239 (ptp-170) cc_final: 0.7007 (ptp90)
REVERT: C  255 LYS cc_start: 0.8028 (tttm) cc_final: 0.7827 (ttpp)
REVERT: C  314 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8398 (tm-30)
REVERT: B  187 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8186 (ptp-110)
REVERT: B  255 LYS cc_start: 0.8239 (tttm) cc_final: 0.7723 (mttm)
REVERT: B  314 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8211 (tm-30)
REVERT: B  411 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6483 (m-10)
  outliers start: 21
  outliers final: 13
  residues processed: 168
  average time/residue: 0.0712
  time to fit residues: 16.6776
Evaluate side-chains
  151 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  411 PHE
Chi-restraints excluded: chain B residue  414 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 86 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
A 225 ASN
C 219 HIS
** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 219 HIS
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.160626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.138470 restraints weight = 12564.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.62
r_work: 0.3570 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7818  Z= 0.138
  Angle     :  0.586   8.552  10749  Z= 0.282
  Chirality :  0.041   0.161   1230
  Planarity :  0.004   0.032   1269
  Dihedral  :  6.983  44.372   1212
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 18.82 %
    Favored  : 76.08 %
  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 (0.29), residues: 933
  helix:  2.59 (0.21), residues: 678
  sheet:  None (None), residues: 0
  loop : -0.37 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 432 
 TYR   0.009   0.001   TYR A 258 
 PHE   0.023   0.001   PHE A 441 
 TRP   0.012   0.001   TRP C 206 
 HIS   0.003   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7818)
  covalent geometry    : angle       0.58580 (10749)
  hydrogen bonds       : bond        0.05737 (  474)
  hydrogen bonds       : angle       3.69506 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 147
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  277 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8148 (mp)
REVERT: A  285 PHE cc_start: 0.7964 (m-10) cc_final: 0.7651 (m-80)
REVERT: A  375 ARG cc_start: 0.7291 (ptp-170) cc_final: 0.6994 (ptp90)
REVERT: C  255 LYS cc_start: 0.8029 (tttm) cc_final: 0.7807 (ttpp)
REVERT: C  314 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8392 (tm-30)
REVERT: B  187 ARG cc_start: 0.8473 (ptp-110) cc_final: 0.8185 (ptp-110)
REVERT: B  255 LYS cc_start: 0.8248 (tttm) cc_final: 0.7712 (mttm)
REVERT: B  314 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8207 (tm-30)
REVERT: B  375 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6949 (ptp90)
  outliers start: 39
  outliers final: 30
  residues processed: 172
  average time/residue: 0.0711
  time to fit residues: 16.9330
Evaluate side-chains
  171 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  414 CYS
Chi-restraints excluded: chain B residue  483 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 41 optimal weight:    0.2980
   chunk 24 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
C 225 ASN
B 219 HIS
B 225 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.160943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139042 restraints weight = 12430.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.61
r_work: 0.3568 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7818  Z= 0.136
  Angle     :  0.581   7.967  10749  Z= 0.280
  Chirality :  0.041   0.144   1230
  Planarity :  0.004   0.031   1269
  Dihedral  :  6.865  47.739   1212
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 21.05 %
    Favored  : 73.33 %
  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:  2.61 (0.29), residues: 933
  helix:  2.53 (0.21), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.60 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 432 
 TYR   0.009   0.001   TYR A 258 
 PHE   0.023   0.001   PHE B 441 
 TRP   0.012   0.001   TRP C 206 
 HIS   0.003   0.001   HIS B 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7818)
  covalent geometry    : angle       0.58075 (10749)
  hydrogen bonds       : bond        0.05513 (  474)
  hydrogen bonds       : angle       3.63809 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 150
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6017 (m-80)
REVERT: A  277 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8164 (mp)
REVERT: A  285 PHE cc_start: 0.7996 (m-10) cc_final: 0.7751 (m-80)
REVERT: A  375 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6935 (ptp90)
REVERT: C  249 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6353 (m-80)
REVERT: C  255 LYS cc_start: 0.8045 (tttm) cc_final: 0.7818 (ttpp)
REVERT: C  285 PHE cc_start: 0.7808 (m-10) cc_final: 0.7567 (m-80)
REVERT: B  187 ARG cc_start: 0.8509 (ptp-110) cc_final: 0.8164 (ptp-110)
REVERT: B  249 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6140 (m-80)
REVERT: B  255 LYS cc_start: 0.8264 (tttm) cc_final: 0.7703 (mttm)
REVERT: B  314 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8301 (tm-30)
REVERT: B  375 ARG cc_start: 0.7130 (ptp-170) cc_final: 0.6895 (ptp90)
  outliers start: 43
  outliers final: 28
  residues processed: 175
  average time/residue: 0.0716
  time to fit residues: 17.4748
Evaluate side-chains
  179 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  412 ASP
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  414 CYS
Chi-restraints excluded: chain B residue  483 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.161923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140324 restraints weight = 12364.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 2.61
r_work: 0.3585 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7818  Z= 0.130
  Angle     :  0.585   7.934  10749  Z= 0.278
  Chirality :  0.041   0.147   1230
  Planarity :  0.004   0.029   1269
  Dihedral  :  6.823  49.640   1212
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 20.92 %
    Favored  : 73.59 %
  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:  2.53 (0.29), residues: 933
  helix:  2.48 (0.21), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.70 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 187 
 TYR   0.013   0.001   TYR C 390 
 PHE   0.016   0.001   PHE C 450 
 TRP   0.013   0.001   TRP C 206 
 HIS   0.003   0.001   HIS C 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7818)
  covalent geometry    : angle       0.58526 (10749)
  hydrogen bonds       : bond        0.05235 (  474)
  hydrogen bonds       : angle       3.61270 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 151
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6020 (m-80)
REVERT: A  277 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8155 (mp)
REVERT: A  375 ARG cc_start: 0.7231 (ptp-170) cc_final: 0.6902 (ptp90)
REVERT: C  249 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6321 (m-80)
REVERT: C  255 LYS cc_start: 0.8046 (tttm) cc_final: 0.7819 (ttpp)
REVERT: C  285 PHE cc_start: 0.7801 (m-10) cc_final: 0.7592 (m-80)
REVERT: B  187 ARG cc_start: 0.8507 (ptp-110) cc_final: 0.8140 (ptp-110)
REVERT: B  249 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6144 (m-80)
REVERT: B  255 LYS cc_start: 0.8251 (tttm) cc_final: 0.7693 (mttm)
REVERT: B  314 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8311 (tm-30)
REVERT: B  375 ARG cc_start: 0.7070 (ptp-170) cc_final: 0.6814 (ptp90)
  outliers start: 42
  outliers final: 30
  residues processed: 178
  average time/residue: 0.0723
  time to fit residues: 18.1532
Evaluate side-chains
  181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  411 PHE
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  414 CYS
Chi-restraints excluded: chain B residue  430 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.161150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.140394 restraints weight = 12477.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.49
r_work: 0.3572 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7818  Z= 0.140
  Angle     :  0.608   8.073  10749  Z= 0.288
  Chirality :  0.041   0.145   1230
  Planarity :  0.004   0.028   1269
  Dihedral  :  6.867  50.689   1212
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 20.39 %
    Favored  : 73.20 %
  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:  2.41 (0.29), residues: 933
  helix:  2.40 (0.21), residues: 684
  sheet:  None (None), residues: 0
  loop : -0.74 (0.37), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 432 
 TYR   0.017   0.001   TYR B 390 
 PHE   0.018   0.001   PHE B 450 
 TRP   0.012   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7818)
  covalent geometry    : angle       0.60778 (10749)
  hydrogen bonds       : bond        0.05507 (  474)
  hydrogen bonds       : angle       3.67001 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 151
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6065 (m-80)
REVERT: A  277 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8164 (mp)
REVERT: A  375 ARG cc_start: 0.7306 (ptp-170) cc_final: 0.6970 (ptp90)
REVERT: C  249 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6330 (m-80)
REVERT: C  255 LYS cc_start: 0.8035 (tttm) cc_final: 0.7796 (ttpp)
REVERT: B  249 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6177 (m-80)
REVERT: B  285 PHE cc_start: 0.7851 (m-10) cc_final: 0.7580 (m-80)
REVERT: B  314 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8314 (tm-30)
REVERT: B  375 ARG cc_start: 0.7110 (ptp-170) cc_final: 0.6852 (ptp90)
REVERT: B  390 TYR cc_start: 0.7599 (t80) cc_final: 0.7346 (t80)
  outliers start: 49
  outliers final: 37
  residues processed: 178
  average time/residue: 0.0715
  time to fit residues: 17.6895
Evaluate side-chains
  186 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 145
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  411 PHE
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  412 ASP
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  414 CYS
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 87 optimal weight:    0.3980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.141600 restraints weight = 12516.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.62
r_work: 0.3588 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7818  Z= 0.131
  Angle     :  0.607   7.855  10749  Z= 0.286
  Chirality :  0.041   0.145   1230
  Planarity :  0.004   0.027   1269
  Dihedral  :  6.812  52.914   1212
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 20.92 %
    Favored  : 73.33 %
  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:  2.39 (0.29), residues: 933
  helix:  2.35 (0.21), residues: 690
  sheet:  None (None), residues: 0
  loop : -0.73 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.012   0.001   TYR B 390 
 PHE   0.022   0.001   PHE A 184 
 TRP   0.014   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7818)
  covalent geometry    : angle       0.60729 (10749)
  hydrogen bonds       : bond        0.05078 (  474)
  hydrogen bonds       : angle       3.58435 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 150
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6087 (m-80)
REVERT: A  277 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8167 (mp)
REVERT: A  285 PHE cc_start: 0.7932 (m-80) cc_final: 0.7707 (m-80)
REVERT: A  375 ARG cc_start: 0.7186 (ptp-170) cc_final: 0.6854 (ptp90)
REVERT: C  249 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6352 (m-80)
REVERT: C  255 LYS cc_start: 0.8037 (tttm) cc_final: 0.7804 (ttpp)
REVERT: C  285 PHE cc_start: 0.7932 (m-80) cc_final: 0.7641 (m-80)
REVERT: B  249 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6161 (m-80)
REVERT: B  277 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: B  285 PHE cc_start: 0.7821 (m-10) cc_final: 0.7587 (m-80)
REVERT: B  314 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8317 (tm-30)
REVERT: B  375 ARG cc_start: 0.7055 (ptp-170) cc_final: 0.6794 (ptp90)
  outliers start: 44
  outliers final: 33
  residues processed: 176
  average time/residue: 0.0719
  time to fit residues: 18.0016
Evaluate side-chains
  187 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 149
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  411 PHE
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  412 ASP
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  449 THR
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  414 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.156545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134575 restraints weight = 12520.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.61
r_work: 0.3517 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7818  Z= 0.169
  Angle     :  0.660   9.083  10749  Z= 0.315
  Chirality :  0.043   0.152   1230
  Planarity :  0.004   0.029   1269
  Dihedral  :  7.010  52.696   1212
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 20.92 %
    Favored  : 73.20 %
  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:  2.35 (0.29), residues: 933
  helix:  2.33 (0.21), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.73 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 187 
 TYR   0.010   0.001   TYR A 258 
 PHE   0.025   0.002   PHE B 450 
 TRP   0.011   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7818)
  covalent geometry    : angle       0.65977 (10749)
  hydrogen bonds       : bond        0.06571 (  474)
  hydrogen bonds       : angle       3.84417 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 140
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6164 (m-80)
REVERT: A  277 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (mp)
REVERT: A  375 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.7040 (ptp90)
REVERT: C  249 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6439 (m-80)
REVERT: C  301 MET cc_start: 0.7275 (tpt) cc_final: 0.6532 (tpp)
REVERT: C  390 TYR cc_start: 0.7635 (t80) cc_final: 0.7378 (t80)
REVERT: B  249 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6284 (m-80)
REVERT: B  277 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: B  314 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8288 (tm-30)
REVERT: B  375 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.7010 (ptp90)
REVERT: B  390 TYR cc_start: 0.7585 (t80) cc_final: 0.7363 (t80)
  outliers start: 45
  outliers final: 34
  residues processed: 172
  average time/residue: 0.0691
  time to fit residues: 16.7222
Evaluate side-chains
  177 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 138
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  412 ASP
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  449 THR
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain C residue  483 THR
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  414 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    0.0570
   chunk 35 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 88 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.0902

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.159133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.137198 restraints weight = 12431.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 2.63
r_work: 0.3550 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7818  Z= 0.144
  Angle     :  0.634   8.282  10749  Z= 0.302
  Chirality :  0.041   0.153   1230
  Planarity :  0.004   0.028   1269
  Dihedral  :  7.064  57.087   1212
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.70 %
    Favored  : 73.33 %
  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:  2.37 (0.29), residues: 933
  helix:  2.35 (0.21), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.74 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 187 
 TYR   0.019   0.001   TYR A 390 
 PHE   0.017   0.001   PHE B 450 
 TRP   0.013   0.001   TRP A 206 
 HIS   0.004   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7818)
  covalent geometry    : angle       0.63380 (10749)
  hydrogen bonds       : bond        0.05709 (  474)
  hydrogen bonds       : angle       3.70044 ( 1404)

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

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

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1866 Ramachandran restraints generated.
    933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  249 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6124 (m-80)
REVERT: A  277 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8123 (mp)
REVERT: A  375 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6839 (ptp90)
REVERT: A  426 TYR cc_start: 0.8617 (t80) cc_final: 0.8344 (t80)
REVERT: C  249 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6450 (m-80)
REVERT: C  255 LYS cc_start: 0.8037 (tttm) cc_final: 0.7810 (ttpp)
REVERT: C  390 TYR cc_start: 0.7590 (t80) cc_final: 0.7336 (t80)
REVERT: B  249 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6254 (m-80)
REVERT: B  277 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8097 (mp)
REVERT: B  285 PHE cc_start: 0.7925 (m-10) cc_final: 0.7600 (m-80)
REVERT: B  314 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8323 (tm-30)
REVERT: B  375 ARG cc_start: 0.7234 (ptp-170) cc_final: 0.6977 (ptp90)
REVERT: B  390 TYR cc_start: 0.7522 (t80) cc_final: 0.7301 (t80)
  outliers start: 38
  outliers final: 32
  residues processed: 166
  average time/residue: 0.0665
  time to fit residues: 15.3714
Evaluate side-chains
  178 residues out of total 813 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 141
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  220 ILE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  249 PHE
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  414 CYS
Chi-restraints excluded: chain C residue  195 ILE
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  215 THR
Chi-restraints excluded: chain C residue  244 ILE
Chi-restraints excluded: chain C residue  249 PHE
Chi-restraints excluded: chain C residue  298 CYS
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  353 VAL
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  412 ASP
Chi-restraints excluded: chain C residue  414 CYS
Chi-restraints excluded: chain C residue  449 THR
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  231 PHE
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  249 PHE
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  298 CYS
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  353 VAL
Chi-restraints excluded: chain B residue  372 LEU
Chi-restraints excluded: chain B residue  406 THR
Chi-restraints excluded: chain B residue  412 ASP
Chi-restraints excluded: chain B residue  414 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 92 optimal weight:    9.9990
   chunk 4 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 219 HIS
C 219 HIS
B 219 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.162507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.140944 restraints weight = 12382.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.61
r_work: 0.3588 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7818  Z= 0.130
  Angle     :  0.619   7.983  10749  Z= 0.291
  Chirality :  0.041   0.151   1230
  Planarity :  0.004   0.027   1269
  Dihedral  :  6.996  57.934   1212
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.70 %
    Favored  : 73.33 %
  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:  2.33 (0.29), residues: 933
  helix:  2.35 (0.21), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.85 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 187 
 TYR   0.007   0.001   TYR A 390 
 PHE   0.026   0.001   PHE A 184 
 TRP   0.014   0.001   TRP A 206 
 HIS   0.003   0.001   HIS A 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7818)
  covalent geometry    : angle       0.61944 (10749)
  hydrogen bonds       : bond        0.04975 (  474)
  hydrogen bonds       : angle       3.57871 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1389.03 seconds
wall clock time: 24 minutes 34.21 seconds (1474.21 seconds total)