Starting phenix.real_space_refine
on Wed Jan 15 13:55:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja5_61290/01_2025/9ja5_61290.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.022 sd=   1.765
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    5148      2.51       5
     N    1518      2.21       5
     O    1761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8469
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 1391
          Classifications: {'peptide': 167}
          Link IDs: {'PTRANS': 6, 'TRANS': 160}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "C"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
    Chain: "D"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
    Chain: "E"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 24
          Classifications: {'water': 24}
          Link IDs: {None: 23}
    Chain: "F"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 25
          Classifications: {'water': 25}
          Link IDs: {None: 24}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.05, per 1000 atoms: 0.48
  Number of scatterers: 8469
  At special positions: 0
  Unit cell: (85.6, 78.4, 210.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1761      8.00
     N    1518      7.00
     C    5148      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: 2.06
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      72.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 211 through 275
      removed outlier: 3.983A  pdb=" N   GLU A 227 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.833A  pdb=" N   SER A 305 " --> pdb=" O   GLU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 318
      removed outlier: 3.926A  pdb=" N   ARG A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR A 314 " --> pdb=" O   ASN A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 329
      removed outlier: 3.917A  pdb=" N   LEU A 329 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 329'
    Processing helix  chain 'A' and resid 330 through 339
    Processing helix  chain 'A' and resid 342 through 347
      removed outlier: 3.653A  pdb=" N   SER A 347 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 546
      removed outlier: 3.876A  pdb=" N   PHE A 546 " --> pdb=" O   GLN A 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 275
      removed outlier: 3.984A  pdb=" N   GLU B 227 " --> pdb=" O   LYS B 223 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN B 248 " --> pdb=" O   ARG B 244 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU B 253 " --> pdb=" O   ASP B 249 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.833A  pdb=" N   SER B 305 " --> pdb=" O   GLU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 318
      removed outlier: 3.927A  pdb=" N   ARG B 313 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR B 314 " --> pdb=" O   ASN B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 329
      removed outlier: 3.917A  pdb=" N   LEU B 329 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 326 through 329'
    Processing helix  chain 'B' and resid 330 through 339
    Processing helix  chain 'B' and resid 342 through 347
      removed outlier: 3.653A  pdb=" N   SER B 347 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 546
      removed outlier: 3.877A  pdb=" N   PHE B 546 " --> pdb=" O   GLN B 542 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 275
      removed outlier: 3.983A  pdb=" N   GLU C 227 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASN C 248 " --> pdb=" O   ARG C 244 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU C 253 " --> pdb=" O   ASP C 249 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG C 255 " --> pdb=" O   SER C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 305
      removed outlier: 3.832A  pdb=" N   SER C 305 " --> pdb=" O   GLU C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 309 through 318
      removed outlier: 3.927A  pdb=" N   ARG C 313 " --> pdb=" O   GLU C 309 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR C 314 " --> pdb=" O   ASN C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 329
      removed outlier: 3.917A  pdb=" N   LEU C 329 " --> pdb=" O   ASP C 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 326 through 329'
    Processing helix  chain 'C' and resid 330 through 339
    Processing helix  chain 'C' and resid 342 through 347
      removed outlier: 3.654A  pdb=" N   SER C 347 " --> pdb=" O   ALA C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 528 through 546
      removed outlier: 3.876A  pdb=" N   PHE C 546 " --> pdb=" O   GLN C 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 212 through 275
      removed outlier: 3.983A  pdb=" N   GLU D 227 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU D 253 " --> pdb=" O   ASP D 249 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG D 255 " --> pdb=" O   SER D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 305
      removed outlier: 3.833A  pdb=" N   SER D 305 " --> pdb=" O   GLU D 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 309 through 318
      removed outlier: 3.927A  pdb=" N   ARG D 313 " --> pdb=" O   GLU D 309 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR D 314 " --> pdb=" O   ASN D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 326 through 329
      removed outlier: 3.918A  pdb=" N   LEU D 329 " --> pdb=" O   ASP D 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 326 through 329'
    Processing helix  chain 'D' and resid 330 through 339
    Processing helix  chain 'D' and resid 342 through 347
      removed outlier: 3.654A  pdb=" N   SER D 347 " --> pdb=" O   ALA D 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 528 through 546
      removed outlier: 3.876A  pdb=" N   PHE D 546 " --> pdb=" O   GLN D 542 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 212 through 275
      removed outlier: 3.983A  pdb=" N   GLU E 227 " --> pdb=" O   LYS E 223 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN E 248 " --> pdb=" O   ARG E 244 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU E 253 " --> pdb=" O   ASP E 249 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   ARG E 255 " --> pdb=" O   SER E 251 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 299 through 305
      removed outlier: 3.833A  pdb=" N   SER E 305 " --> pdb=" O   GLU E 301 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 309 through 318
      removed outlier: 3.927A  pdb=" N   ARG E 313 " --> pdb=" O   GLU E 309 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR E 314 " --> pdb=" O   ASN E 310 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 326 through 329
      removed outlier: 3.917A  pdb=" N   LEU E 329 " --> pdb=" O   ASP E 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 326 through 329'
    Processing helix  chain 'E' and resid 330 through 339
    Processing helix  chain 'E' and resid 342 through 347
      removed outlier: 3.654A  pdb=" N   SER E 347 " --> pdb=" O   ALA E 343 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 528 through 546
      removed outlier: 3.876A  pdb=" N   PHE E 546 " --> pdb=" O   GLN E 542 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 212 through 275
      removed outlier: 3.983A  pdb=" N   GLU F 227 " --> pdb=" O   LYS F 223 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASN F 248 " --> pdb=" O   ARG F 244 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LEU F 253 " --> pdb=" O   ASP F 249 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG F 255 " --> pdb=" O   SER F 251 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 299 through 305
      removed outlier: 3.833A  pdb=" N   SER F 305 " --> pdb=" O   GLU F 301 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 309 through 318
      removed outlier: 3.927A  pdb=" N   ARG F 313 " --> pdb=" O   GLU F 309 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   TYR F 314 " --> pdb=" O   ASN F 310 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 329
      removed outlier: 3.918A  pdb=" N   LEU F 329 " --> pdb=" O   ASP F 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 326 through 329'
    Processing helix  chain 'F' and resid 330 through 339
    Processing helix  chain 'F' and resid 342 through 347
      removed outlier: 3.653A  pdb=" N   SER F 347 " --> pdb=" O   ALA F 343 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 528 through 546
      removed outlier: 3.876A  pdb=" N   PHE F 546 " --> pdb=" O   GLN F 542 " (cutoff:3.500A)

    499 hydrogen bonds defined for protein.
    1497 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.94

  Time building geometry restraints manager: 2.38 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: 2739
        1.33 -     1.45: 1018
        1.45 -     1.56: 4637
        1.56 -     1.68: 0
        1.68 -     1.80: 78
  Bond restraints: 8472
  Sorted by residual:
  bond pdb=" C   LEU E 306 "
       pdb=" N   SER E 307 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.045 1.73e-02 3.34e+03 6.92e+00
  bond pdb=" C   LEU F 306 "
       pdb=" N   SER F 307 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.045 1.73e-02 3.34e+03 6.86e+00
  bond pdb=" C   LEU A 306 "
       pdb=" N   SER A 307 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.045 1.73e-02 3.34e+03 6.86e+00
  bond pdb=" C   LEU B 306 "
       pdb=" N   SER B 307 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.045 1.73e-02 3.34e+03 6.84e+00
  bond pdb=" C   LEU C 306 "
       pdb=" N   SER C 307 "
    ideal  model  delta    sigma   weight residual
    1.333  1.287  0.045 1.73e-02 3.34e+03 6.83e+00
  ... (remaining 8467 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 10499
        1.79 -     3.58: 703
        3.58 -     5.38: 110
        5.38 -     7.17: 52
        7.17 -     8.96: 42
  Bond angle restraints: 11406
  Sorted by residual:
  angle pdb=" C   PHE E 285 "
        pdb=" CA  PHE E 285 "
        pdb=" CB  PHE E 285 "
      ideal   model   delta    sigma   weight residual
     110.42  101.46    8.96 1.99e+00 2.53e-01 2.03e+01
  angle pdb=" C   PHE A 285 "
        pdb=" CA  PHE A 285 "
        pdb=" CB  PHE A 285 "
      ideal   model   delta    sigma   weight residual
     110.42  101.48    8.94 1.99e+00 2.53e-01 2.02e+01
  angle pdb=" C   PHE D 285 "
        pdb=" CA  PHE D 285 "
        pdb=" CB  PHE D 285 "
      ideal   model   delta    sigma   weight residual
     110.42  101.49    8.93 1.99e+00 2.53e-01 2.01e+01
  angle pdb=" C   PHE C 285 "
        pdb=" CA  PHE C 285 "
        pdb=" CB  PHE C 285 "
      ideal   model   delta    sigma   weight residual
     110.42  101.50    8.92 1.99e+00 2.53e-01 2.01e+01
  angle pdb=" C   PHE B 285 "
        pdb=" CA  PHE B 285 "
        pdb=" CB  PHE B 285 "
      ideal   model   delta    sigma   weight residual
     110.42  101.52    8.90 1.99e+00 2.53e-01 2.00e+01
  ... (remaining 11401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.19: 4433
       14.19 -    28.38: 679
       28.38 -    42.56: 144
       42.56 -    56.75: 24
       56.75 -    70.94: 18
  Dihedral angle restraints: 5298
    sinusoidal: 2322
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" CA  PHE C 285 "
           pdb=" C   PHE C 285 "
           pdb=" N   ASN C 286 "
           pdb=" CA  ASN C 286 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.08  -21.92     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  PHE D 285 "
           pdb=" C   PHE D 285 "
           pdb=" N   ASN D 286 "
           pdb=" CA  ASN D 286 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.10  -21.90     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  PHE B 285 "
           pdb=" C   PHE B 285 "
           pdb=" N   ASN B 286 "
           pdb=" CA  ASN B 286 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.10  -21.90     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 5295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 419
       0.037 -    0.073: 535
       0.073 -    0.110: 171
       0.110 -    0.146: 63
       0.146 -    0.183: 36
  Chirality restraints: 1224
  Sorted by residual:
  chirality pdb=" CA  GLU E 238 "
            pdb=" N   GLU E 238 "
            pdb=" C   GLU E 238 "
            pdb=" CB  GLU E 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  SER A 307 "
            pdb=" N   SER A 307 "
            pdb=" C   SER A 307 "
            pdb=" CB  SER A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.17e-01
  chirality pdb=" CA  GLU A 238 "
            pdb=" N   GLU A 238 "
            pdb=" C   GLU A 238 "
            pdb=" CB  GLU A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.11e-01
  ... (remaining 1221 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 285 "   -0.035 2.00e-02 2.50e+03   2.92e-02 1.50e+01
        pdb=" CG  PHE D 285 "    0.068 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 285 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 285 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 285 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 285 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 285 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 285 "    0.034 2.00e-02 2.50e+03   2.92e-02 1.49e+01
        pdb=" CG  PHE C 285 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 285 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 285 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 285 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 285 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 285 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 285 "   -0.034 2.00e-02 2.50e+03   2.92e-02 1.49e+01
        pdb=" CG  PHE F 285 "    0.067 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 285 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 285 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 285 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 285 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 285 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 316
        2.67 -     3.23: 8692
        3.23 -     3.79: 12514
        3.79 -     4.34: 16572
        4.34 -     4.90: 27000
  Nonbonded interactions: 65094
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 309 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OE2 GLU D 309 "
            pdb=" O   HOH D 701 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   SER A 307 "
            pdb=" OG  SER A 307 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   SER D 307 "
            pdb=" OG  SER D 307 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   SER F 307 "
            pdb=" OG  SER F 307 "
     model   vdw
     2.126 3.040
  ... (remaining 65089 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             7.080
  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:          0.370
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     19.400
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.014   0.066   8472  Z= 0.921
  Angle     :  1.154   8.958  11406  Z= 0.626
  Chirality :  0.064   0.183   1224
  Planarity :  0.005   0.029   1518
  Dihedral  : 14.299  70.938   3342
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.25), residues: 978
  helix: -0.98 (0.18), residues: 714
  sheet:  None (None), residues: 0
  loop : -3.96 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.006   TRP D 221 
 PHE   0.068   0.005   PHE D 285 
 TYR   0.026   0.004   TYR B 314 
 ARG   0.009   0.001   ARG D 215 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A  245 ASP cc_start: 0.7624 (m-30) cc_final: 0.7160 (t0)
REVERT: A  301 GLU cc_start: 0.8565 (mp0) cc_final: 0.8319 (mp0)
REVERT: A  308 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8698 (tp30)
REVERT: A  309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: A  323 ASP cc_start: 0.8256 (t0) cc_final: 0.7920 (t0)
REVERT: A  527 LEU cc_start: 0.9275 (mp) cc_final: 0.9040 (mp)
REVERT: A  531 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7617 (mt-10)
REVERT: B  245 ASP cc_start: 0.7507 (m-30) cc_final: 0.7264 (t0)
REVERT: B  309 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: B  323 ASP cc_start: 0.8209 (t0) cc_final: 0.8009 (t0)
REVERT: C  245 ASP cc_start: 0.7803 (m-30) cc_final: 0.6917 (OUTLIER)
REVERT: C  309 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: C  323 ASP cc_start: 0.8037 (t0) cc_final: 0.7544 (t0)
REVERT: C  326 ASP cc_start: 0.8389 (t0) cc_final: 0.7931 (t0)
REVERT: D  245 ASP cc_start: 0.7634 (m-30) cc_final: 0.7380 (OUTLIER)
REVERT: D  309 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7308 (tm-30)
REVERT: D  323 ASP cc_start: 0.8208 (t0) cc_final: 0.7863 (t0)
REVERT: D  326 ASP cc_start: 0.8369 (t0) cc_final: 0.8098 (t70)
REVERT: D  527 LEU cc_start: 0.9139 (mp) cc_final: 0.8805 (mt)
REVERT: D  531 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7471 (mt-10)
REVERT: E  324 GLU cc_start: 0.8450 (tp30) cc_final: 0.7783 (tp30)
REVERT: E  534 GLU cc_start: 0.7828 (tp30) cc_final: 0.7434 (tp30)
REVERT: F  245 ASP cc_start: 0.7919 (m-30) cc_final: 0.7253 (OUTLIER)
REVERT: F  309 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7389 (tm-30)
REVERT: F  323 ASP cc_start: 0.8135 (t0) cc_final: 0.7733 (t0)
REVERT: F  326 ASP cc_start: 0.8488 (t0) cc_final: 0.8106 (t0)
  outliers start: 0
  outliers final: 3
  residues processed: 249
  average time/residue: 1.6069
  time to fit residues: 418.8425
Evaluate side-chains
  213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0870
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0000
   chunk 29 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0020
   overall best weight:    0.2570

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

Flipped N/Q/H residues before XYZ refinement:
A 243 GLN
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 310 ASN
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 310 ASN
** F 532 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.165470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.121596 restraints weight = 9255.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.69
r_work: 0.3303 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8472  Z= 0.207
  Angle     :  0.660   7.231  11406  Z= 0.347
  Chirality :  0.038   0.156   1224
  Planarity :  0.004   0.041   1518
  Dihedral  :  4.784  17.519   1134
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.03 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.27), residues: 978
  helix:  0.88 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.80 (0.33), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP C 221 
 PHE   0.021   0.002   PHE F 285 
 TYR   0.007   0.001   TYR D 314 
 ARG   0.010   0.001   ARG E 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 230
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A  245 ASP cc_start: 0.7396 (m-30) cc_final: 0.6915 (OUTLIER)
REVERT: A  301 GLU cc_start: 0.8379 (mp0) cc_final: 0.8095 (mp0)
REVERT: A  309 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: A  323 ASP cc_start: 0.7744 (t0) cc_final: 0.7227 (t0)
REVERT: A  527 LEU cc_start: 0.9101 (mp) cc_final: 0.8834 (mp)
REVERT: B  227 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8444 (mp0)
REVERT: B  245 ASP cc_start: 0.7417 (m-30) cc_final: 0.7011 (t0)
REVERT: B  323 ASP cc_start: 0.7837 (t0) cc_final: 0.7406 (t0)
REVERT: C  245 ASP cc_start: 0.7502 (m-30) cc_final: 0.6744 (OUTLIER)
REVERT: C  309 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6558 (tm-30)
REVERT: C  323 ASP cc_start: 0.7596 (t0) cc_final: 0.7121 (t0)
REVERT: D  245 ASP cc_start: 0.7576 (m-30) cc_final: 0.7194 (OUTLIER)
REVERT: D  309 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6827 (tm-30)
REVERT: D  323 ASP cc_start: 0.7668 (t0) cc_final: 0.7174 (t0)
REVERT: F  245 ASP cc_start: 0.7761 (m-30) cc_final: 0.7079 (t0)
REVERT: F  309 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6531 (tm-30)
REVERT: F  316 LYS cc_start: 0.7416 (mttt) cc_final: 0.7206 (mttm)
REVERT: F  323 ASP cc_start: 0.7803 (t0) cc_final: 0.7209 (t0)
REVERT: F  326 ASP cc_start: 0.7534 (t0) cc_final: 0.6966 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 238
  average time/residue: 1.5159
  time to fit residues: 379.3033
Evaluate side-chains
  225 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 218
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain D residue  225 THR
Chi-restraints excluded: chain F residue  286 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.1980
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 58 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.160087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.116651 restraints weight = 9420.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.69
r_work: 0.3233 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8472  Z= 0.224
  Angle     :  0.620   6.886  11406  Z= 0.323
  Chirality :  0.039   0.154   1224
  Planarity :  0.004   0.038   1518
  Dihedral  :  4.480  22.508   1134
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 18.91 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 978
  helix:  1.49 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.59 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 221 
 PHE   0.025   0.002   PHE C 285 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.007   0.001   ARG B 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 225
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  222 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7247 (mmp-170)
REVERT: A  245 ASP cc_start: 0.7412 (m-30) cc_final: 0.6918 (t0)
REVERT: A  308 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: A  309 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6853 (tm-30)
REVERT: A  323 ASP cc_start: 0.7782 (t0) cc_final: 0.7246 (t0)
REVERT: A  345 ASP cc_start: 0.8589 (m-30) cc_final: 0.8333 (m-30)
REVERT: B  222 ARG cc_start: 0.8253 (mmp-170) cc_final: 0.8044 (mmp-170)
REVERT: B  245 ASP cc_start: 0.7366 (m-30) cc_final: 0.7082 (t0)
REVERT: B  308 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8596 (tm-30)
REVERT: B  309 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6498 (tm-30)
REVERT: B  323 ASP cc_start: 0.7926 (t0) cc_final: 0.7482 (t0)
REVERT: C  221 TRP cc_start: 0.6563 (t60) cc_final: 0.6025 (t60)
REVERT: C  222 ARG cc_start: 0.7786 (mmp-170) cc_final: 0.7535 (mmp-170)
REVERT: C  245 ASP cc_start: 0.7557 (m-30) cc_final: 0.6794 (t0)
REVERT: C  308 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8641 (tm-30)
REVERT: C  309 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6683 (tm-30)
REVERT: C  323 ASP cc_start: 0.7678 (t0) cc_final: 0.7065 (t0)
REVERT: D  245 ASP cc_start: 0.7598 (m-30) cc_final: 0.7194 (t0)
REVERT: D  308 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8654 (tm-30)
REVERT: D  309 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6748 (tm-30)
REVERT: D  323 ASP cc_start: 0.7792 (t0) cc_final: 0.7248 (t0)
REVERT: E  309 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6582 (tm-30)
REVERT: E  323 ASP cc_start: 0.7893 (t0) cc_final: 0.7451 (t0)
REVERT: F  245 ASP cc_start: 0.7818 (m-30) cc_final: 0.7061 (t0)
REVERT: F  309 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: F  323 ASP cc_start: 0.7873 (t0) cc_final: 0.7356 (t0)
REVERT: F  326 ASP cc_start: 0.7513 (t0) cc_final: 0.6986 (t0)
  outliers start: 13
  outliers final: 9
  residues processed: 232
  average time/residue: 1.4366
  time to fit residues: 350.5763
Evaluate side-chains
  217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 207
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ARG
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain E residue  530 THR
Chi-restraints excluded: chain F residue  298 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.159624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.115981 restraints weight = 9300.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.68
r_work: 0.3215 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8472  Z= 0.242
  Angle     :  0.620   9.303  11406  Z= 0.317
  Chirality :  0.039   0.152   1224
  Planarity :  0.004   0.031   1518
  Dihedral  :  4.403  22.957   1134
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 20.19 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.28), residues: 978
  helix:  1.73 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.54 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP B 221 
 PHE   0.024   0.002   PHE F 285 
 TYR   0.006   0.001   TYR F 314 
 ARG   0.008   0.000   ARG C 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 211
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7407 (m-30) cc_final: 0.6908 (t0)
REVERT: A  308 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: A  309 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6727 (tm-30)
REVERT: A  323 ASP cc_start: 0.7758 (t0) cc_final: 0.7195 (t0)
REVERT: B  245 ASP cc_start: 0.7362 (m-30) cc_final: 0.6924 (t0)
REVERT: B  308 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: B  309 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6405 (tm-30)
REVERT: B  323 ASP cc_start: 0.7902 (t0) cc_final: 0.7444 (t0)
REVERT: C  221 TRP cc_start: 0.6749 (t60) cc_final: 0.6116 (t60)
REVERT: C  245 ASP cc_start: 0.7507 (m-30) cc_final: 0.6730 (t0)
REVERT: C  249 ASP cc_start: 0.8049 (m-30) cc_final: 0.7723 (m-30)
REVERT: C  308 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8583 (tm-30)
REVERT: C  309 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6597 (tm-30)
REVERT: C  323 ASP cc_start: 0.7709 (t0) cc_final: 0.7131 (t0)
REVERT: D  245 ASP cc_start: 0.7599 (m-30) cc_final: 0.7171 (t0)
REVERT: D  308 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8556 (tm-30)
REVERT: D  309 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6625 (tm-30)
REVERT: D  323 ASP cc_start: 0.7752 (t0) cc_final: 0.7210 (t0)
REVERT: E  241 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7634 (t0)
REVERT: E  244 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7664 (ttp80)
REVERT: E  308 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8512 (tm-30)
REVERT: F  245 ASP cc_start: 0.7777 (m-30) cc_final: 0.7031 (t0)
REVERT: F  308 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: F  309 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6569 (tm-30)
REVERT: F  323 ASP cc_start: 0.7884 (t0) cc_final: 0.7356 (t0)
REVERT: F  326 ASP cc_start: 0.7461 (t0) cc_final: 0.6940 (t0)
  outliers start: 19
  outliers final: 8
  residues processed: 221
  average time/residue: 1.4549
  time to fit residues: 339.0477
Evaluate side-chains
  212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain D residue  225 THR
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain E residue  530 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0070
   chunk 91 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 243 GLN
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 243 GLN
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 243 GLN
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.160973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.117834 restraints weight = 9503.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.76
r_work: 0.3268 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8472  Z= 0.197
  Angle     :  0.571   8.800  11406  Z= 0.294
  Chirality :  0.037   0.155   1224
  Planarity :  0.003   0.028   1518
  Dihedral  :  4.176  23.616   1134
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.47 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.28), residues: 978
  helix:  2.31 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.12 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 221 
 PHE   0.018   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.010   0.000   ARG B 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 208
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7154 (m-30) cc_final: 0.6643 (t0)
REVERT: A  308 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8445 (tm-30)
REVERT: A  309 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6464 (tm-30)
REVERT: A  323 ASP cc_start: 0.7430 (t0) cc_final: 0.6856 (t0)
REVERT: B  244 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7454 (ttp80)
REVERT: B  245 ASP cc_start: 0.7125 (m-30) cc_final: 0.6905 (t0)
REVERT: B  308 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: B  309 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6424 (tm-30)
REVERT: B  323 ASP cc_start: 0.7645 (t0) cc_final: 0.7193 (t0)
REVERT: C  245 ASP cc_start: 0.7233 (m-30) cc_final: 0.6512 (t0)
REVERT: C  249 ASP cc_start: 0.7833 (m-30) cc_final: 0.7591 (m-30)
REVERT: C  308 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8258 (tm-30)
REVERT: C  309 GLU cc_start: 0.6895 (tm-30) cc_final: 0.6417 (tm-30)
REVERT: C  323 ASP cc_start: 0.7405 (t0) cc_final: 0.6809 (t0)
REVERT: D  211 MET cc_start: 0.8258 (pp-130) cc_final: 0.8015 (pp-130)
REVERT: D  308 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: D  323 ASP cc_start: 0.7472 (t0) cc_final: 0.6889 (t0)
REVERT: E  241 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7493 (t0)
REVERT: E  244 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7381 (ttp80)
REVERT: E  308 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: E  323 ASP cc_start: 0.7579 (t0) cc_final: 0.7079 (t0)
REVERT: F  211 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8058 (pp-130)
REVERT: F  245 ASP cc_start: 0.7543 (m-30) cc_final: 0.6799 (t0)
REVERT: F  308 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8518 (tm-30)
REVERT: F  323 ASP cc_start: 0.7617 (t0) cc_final: 0.7082 (t0)
  outliers start: 22
  outliers final: 8
  residues processed: 220
  average time/residue: 1.3862
  time to fit residues: 321.5170
Evaluate side-chains
  201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 191
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain D residue  286 ASN
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain F residue  211 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.159886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.115459 restraints weight = 9372.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.72
r_work: 0.3206 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8472  Z= 0.257
  Angle     :  0.625  10.399  11406  Z= 0.313
  Chirality :  0.039   0.177   1224
  Planarity :  0.004   0.037   1518
  Dihedral  :  4.337  26.074   1134
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 22.86 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.29), residues: 978
  helix:  2.12 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.34 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 221 
 PHE   0.022   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.008   0.000   ARG A 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7451 (m-30) cc_final: 0.6911 (t0)
REVERT: A  308 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8523 (tm-30)
REVERT: A  309 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6636 (tm-30)
REVERT: A  323 ASP cc_start: 0.7666 (t0) cc_final: 0.7157 (t0)
REVERT: A  527 LEU cc_start: 0.8182 (pt) cc_final: 0.7858 (pp)
REVERT: B  244 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7630 (ttp80)
REVERT: B  245 ASP cc_start: 0.7402 (m-30) cc_final: 0.6953 (t0)
REVERT: B  308 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: B  309 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6618 (tm-30)
REVERT: C  221 TRP cc_start: 0.7162 (t60) cc_final: 0.6783 (t60)
REVERT: C  245 ASP cc_start: 0.7480 (m-30) cc_final: 0.6747 (t0)
REVERT: C  308 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: C  309 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6572 (tm-30)
REVERT: C  323 ASP cc_start: 0.7653 (t0) cc_final: 0.7069 (t0)
REVERT: D  308 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8475 (tm-30)
REVERT: D  309 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6547 (tm-30)
REVERT: D  323 ASP cc_start: 0.7706 (t0) cc_final: 0.7140 (t0)
REVERT: E  241 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7561 (t0)
REVERT: E  244 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7655 (ttp80)
REVERT: E  308 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: F  245 ASP cc_start: 0.7797 (m-30) cc_final: 0.7033 (t0)
REVERT: F  308 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: F  323 ASP cc_start: 0.7852 (t0) cc_final: 0.7337 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 214
  average time/residue: 1.4401
  time to fit residues: 324.4294
Evaluate side-chains
  210 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain D residue  225 THR
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain E residue  530 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.160477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117534 restraints weight = 9505.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.76
r_work: 0.3208 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8472  Z= 0.210
  Angle     :  0.613  10.000  11406  Z= 0.302
  Chirality :  0.038   0.152   1224
  Planarity :  0.004   0.029   1518
  Dihedral  :  4.245  27.003   1134
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 23.61 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.29), residues: 978
  helix:  2.26 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.27 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 221 
 PHE   0.018   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.008   0.000   ARG C 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 213
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7134 (m-30) cc_final: 0.6612 (t0)
REVERT: A  308 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8413 (tm-30)
REVERT: A  309 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6395 (tm-30)
REVERT: A  323 ASP cc_start: 0.7370 (t0) cc_final: 0.6799 (t0)
REVERT: A  527 LEU cc_start: 0.8165 (pt) cc_final: 0.7904 (pp)
REVERT: B  222 ARG cc_start: 0.7559 (mmp-170) cc_final: 0.7182 (mmp-170)
REVERT: B  244 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7424 (ttp80)
REVERT: B  245 ASP cc_start: 0.7150 (m-30) cc_final: 0.6642 (t0)
REVERT: B  308 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: B  309 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6420 (tm-30)
REVERT: B  323 ASP cc_start: 0.7617 (t0) cc_final: 0.7134 (t0)
REVERT: C  245 ASP cc_start: 0.7169 (m-30) cc_final: 0.6399 (t0)
REVERT: C  249 ASP cc_start: 0.7831 (m-30) cc_final: 0.7356 (m-30)
REVERT: C  308 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8199 (tm-30)
REVERT: C  309 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6340 (tm-30)
REVERT: C  323 ASP cc_start: 0.7386 (t0) cc_final: 0.6801 (t0)
REVERT: D  211 MET cc_start: 0.8241 (pp-130) cc_final: 0.8023 (pp-130)
REVERT: D  308 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: D  309 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6282 (tm-30)
REVERT: D  323 ASP cc_start: 0.7443 (t0) cc_final: 0.6852 (t0)
REVERT: E  241 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7399 (t0)
REVERT: E  244 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7419 (ttp80)
REVERT: E  308 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: E  323 ASP cc_start: 0.7557 (t0) cc_final: 0.7062 (t0)
REVERT: F  211 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7813 (pp-130)
REVERT: F  245 ASP cc_start: 0.7516 (m-30) cc_final: 0.6774 (t0)
REVERT: F  308 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8444 (tm-30)
REVERT: F  309 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6179 (tm-30)
REVERT: F  323 ASP cc_start: 0.7550 (t0) cc_final: 0.7016 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 220
  average time/residue: 1.4832
  time to fit residues: 343.6599
Evaluate side-chains
  217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 205
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  286 ASN
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  225 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain E residue  530 THR
Chi-restraints excluded: chain F residue  211 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   chunk 78 optimal weight:    0.0170
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.161150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118318 restraints weight = 9565.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.77
r_work: 0.3218 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8472  Z= 0.204
  Angle     :  0.622  10.102  11406  Z= 0.306
  Chirality :  0.037   0.157   1224
  Planarity :  0.004   0.039   1518
  Dihedral  :  4.188  27.501   1134
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 22.97 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.29), residues: 978
  helix:  2.35 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.24 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 221 
 PHE   0.017   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.007   0.000   ARG C 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7148 (m-30) cc_final: 0.6612 (t0)
REVERT: A  308 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: A  309 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6368 (tm-30)
REVERT: A  323 ASP cc_start: 0.7370 (t0) cc_final: 0.6777 (t0)
REVERT: A  527 LEU cc_start: 0.8369 (pt) cc_final: 0.8032 (pp)
REVERT: B  237 ARG cc_start: 0.7246 (mmt90) cc_final: 0.6720 (mpt180)
REVERT: B  244 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7457 (ttp80)
REVERT: B  245 ASP cc_start: 0.7126 (m-30) cc_final: 0.6625 (t0)
REVERT: B  308 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: B  309 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6333 (tm-30)
REVERT: B  323 ASP cc_start: 0.7606 (t0) cc_final: 0.7128 (t0)
REVERT: C  308 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: C  309 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6333 (tm-30)
REVERT: C  323 ASP cc_start: 0.7351 (t0) cc_final: 0.6760 (t0)
REVERT: D  308 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: D  323 ASP cc_start: 0.7454 (t0) cc_final: 0.6885 (t0)
REVERT: E  241 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7391 (t0)
REVERT: E  244 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7453 (ttp80)
REVERT: E  308 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: E  323 ASP cc_start: 0.7545 (t0) cc_final: 0.7040 (t0)
REVERT: F  211 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7767 (pp-130)
REVERT: F  221 TRP cc_start: 0.7687 (t60) cc_final: 0.7445 (t60)
REVERT: F  245 ASP cc_start: 0.7513 (m-30) cc_final: 0.6763 (t0)
REVERT: F  308 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: F  323 ASP cc_start: 0.7524 (t0) cc_final: 0.7028 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 214
  average time/residue: 1.4546
  time to fit residues: 327.7076
Evaluate side-chains
  205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 192
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain B residue  215 ARG
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  530 THR
Chi-restraints excluded: chain F residue  211 MET
Chi-restraints excluded: chain F residue  286 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 63 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 92 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.161081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.118133 restraints weight = 9550.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.78
r_work: 0.3240 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8472  Z= 0.217
  Angle     :  0.641  10.469  11406  Z= 0.314
  Chirality :  0.038   0.177   1224
  Planarity :  0.004   0.059   1518
  Dihedral  :  4.270  30.206   1134
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 23.08 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.29), residues: 978
  helix:  2.41 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.21 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP C 221 
 PHE   0.018   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.007   0.000   ARG C 215 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 ASP cc_start: 0.7182 (m-30) cc_final: 0.6642 (t0)
REVERT: A  308 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8411 (tm-30)
REVERT: A  309 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6342 (tm-30)
REVERT: A  323 ASP cc_start: 0.7365 (t0) cc_final: 0.6798 (t0)
REVERT: A  527 LEU cc_start: 0.8419 (pt) cc_final: 0.8109 (pp)
REVERT: B  237 ARG cc_start: 0.7300 (mmt90) cc_final: 0.6886 (mpt180)
REVERT: B  245 ASP cc_start: 0.7167 (m-30) cc_final: 0.6611 (t0)
REVERT: B  308 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: B  309 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6336 (tm-30)
REVERT: B  323 ASP cc_start: 0.7591 (t0) cc_final: 0.7117 (t0)
REVERT: C  308 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: C  309 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6316 (tm-30)
REVERT: C  323 ASP cc_start: 0.7356 (t0) cc_final: 0.6762 (t0)
REVERT: D  308 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: D  323 ASP cc_start: 0.7435 (t0) cc_final: 0.6876 (t0)
REVERT: E  241 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7281 (t0)
REVERT: E  244 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7430 (ttp80)
REVERT: E  308 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8255 (tm-30)
REVERT: F  211 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7708 (pp-130)
REVERT: F  221 TRP cc_start: 0.7842 (t60) cc_final: 0.7595 (t60)
REVERT: F  245 ASP cc_start: 0.7528 (m-30) cc_final: 0.6772 (t0)
REVERT: F  308 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8427 (tm-30)
REVERT: F  323 ASP cc_start: 0.7516 (t0) cc_final: 0.7004 (t0)
  outliers start: 15
  outliers final: 11
  residues processed: 204
  average time/residue: 1.5332
  time to fit residues: 328.8192
Evaluate side-chains
  204 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 191
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain B residue  215 ARG
Chi-restraints excluded: chain B residue  225 THR
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain D residue  286 ASN
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  286 ASN
Chi-restraints excluded: chain E residue  530 THR
Chi-restraints excluded: chain F residue  211 MET
Chi-restraints excluded: chain F residue  286 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 243 GLN
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.159884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.115418 restraints weight = 9416.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.75
r_work: 0.3201 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8472  Z= 0.266
  Angle     :  0.686  11.453  11406  Z= 0.334
  Chirality :  0.039   0.196   1224
  Planarity :  0.004   0.062   1518
  Dihedral  :  4.462  30.243   1134
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 23.29 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.29), residues: 978
  helix:  2.38 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.24 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.081   0.004   TRP C 221 
 PHE   0.022   0.002   PHE D 285 
 TYR   0.005   0.001   TYR B 318 
 ARG   0.010   0.001   ARG C 222 

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

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

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1956 Ramachandran restraints generated.
    978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 0.953 
Fit side-chains
REVERT: A  245 ASP cc_start: 0.7496 (m-30) cc_final: 0.6942 (t0)
REVERT: A  308 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8499 (tm-30)
REVERT: A  309 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6590 (tm-30)
REVERT: A  323 ASP cc_start: 0.7616 (t0) cc_final: 0.7090 (t0)
REVERT: A  527 LEU cc_start: 0.8499 (pt) cc_final: 0.8186 (pp)
REVERT: B  237 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7120 (mpt180)
REVERT: B  245 ASP cc_start: 0.7429 (m-30) cc_final: 0.6891 (t0)
REVERT: B  308 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: B  309 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6550 (tm-30)
REVERT: B  323 ASP cc_start: 0.7836 (t0) cc_final: 0.7381 (t0)
REVERT: C  308 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: C  309 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6536 (tm-30)
REVERT: C  323 ASP cc_start: 0.7607 (t0) cc_final: 0.7035 (t0)
REVERT: D  308 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: D  309 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6535 (tm-30)
REVERT: D  323 ASP cc_start: 0.7694 (t0) cc_final: 0.7150 (t0)
REVERT: E  241 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (t0)
REVERT: E  244 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7644 (ttp80)
REVERT: E  308 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: E  323 ASP cc_start: 0.7840 (t0) cc_final: 0.7361 (t0)
REVERT: F  211 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7636 (pp-130)
REVERT: F  221 TRP cc_start: 0.7951 (t60) cc_final: 0.7732 (t60)
REVERT: F  245 ASP cc_start: 0.7816 (m-30) cc_final: 0.7046 (t0)
REVERT: F  308 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: F  323 ASP cc_start: 0.7764 (t0) cc_final: 0.7279 (t0)
  outliers start: 16
  outliers final: 8
  residues processed: 197
  average time/residue: 1.5448
  time to fit residues: 319.5883
Evaluate side-chains
  198 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 188
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  534 GLU
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain B residue  286 ASN
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain C residue  286 ASN
Chi-restraints excluded: chain E residue  241 ASP
Chi-restraints excluded: chain E residue  530 THR
Chi-restraints excluded: chain F residue  211 MET
Chi-restraints excluded: chain F residue  286 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 48 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0000
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 243 GLN
** F 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.162654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.118397 restraints weight = 9511.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 2.76
r_work: 0.3239 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8472  Z= 0.217
  Angle     :  0.675  11.679  11406  Z= 0.329
  Chirality :  0.038   0.213   1224
  Planarity :  0.004   0.071   1518
  Dihedral  :  4.385  29.585   1134
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 23.82 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.29), residues: 978
  helix:  2.45 (0.20), residues: 696
  sheet:  None (None), residues: 0
  loop : -2.18 (0.40), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.075   0.004   TRP B 221 
 PHE   0.017   0.002   PHE F 285 
 TYR   0.005   0.001   TYR F 348 
 ARG   0.010   0.000   ARG C 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7833.78 seconds
wall clock time: 138 minutes 47.10 seconds (8327.10 seconds total)