Starting phenix.real_space_refine
on Tue Mar  3 21:29:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2026/6wyl_21968.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5826      2.51       5
     N    1395      2.21       5
     O    1572      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8847
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 2940
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 16, 'TRANS': 380}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.66, per 1000 atoms: 0.19
  Number of scatterers: 8847
  At special positions: 0
  Unit cell: (111.418, 104.516, 77.894, 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      54     16.00
     O    1572      8.00
     N    1395      7.00
     C    5826      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 286.6 milliseconds
  

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      90.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 32
      removed outlier: 3.543A  pdb=" N   HIS A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 73
      removed outlier: 4.237A  pdb=" N   ALA A  38 " --> pdb=" O   GLY A  34 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   LYS A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR A  41 " --> pdb=" O   ASP A  37 " (cutoff:3.500A)
      Proline residue:  A  45  - end of helix
      removed outlier: 3.827A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A  53 " --> pdb=" O   LEU A  49 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      Proline residue:  A  60  - end of helix
      removed outlier: 3.674A  pdb=" N   ILE A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 108
    Processing helix  chain 'A' and resid 131 through 137
      removed outlier: 3.846A  pdb=" N   ILE A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 149
    Processing helix  chain 'A' and resid 150 through 171
      removed outlier: 4.240A  pdb=" N   THR A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 220
      removed outlier: 3.690A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 223 through 255
      removed outlier: 3.694A  pdb=" N   GLU A 227 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU A 228 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 275
      removed outlier: 3.633A  pdb=" N   LYS A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ALA A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 292
      removed outlier: 4.411A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      Proline residue:  A 304  - end of helix
      removed outlier: 3.749A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 330
    Processing helix  chain 'A' and resid 334 through 352
    Processing helix  chain 'A' and resid 357 through 371
      removed outlier: 4.147A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   MET A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 416
      removed outlier: 3.734A  pdb=" N   ILE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ILE A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 32
      removed outlier: 3.544A  pdb=" N   HIS B  32 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 73
      removed outlier: 4.237A  pdb=" N   ALA B  38 " --> pdb=" O   GLY B  34 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   LYS B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   THR B  41 " --> pdb=" O   ASP B  37 " (cutoff:3.500A)
      Proline residue:  B  45  - end of helix
      removed outlier: 3.826A  pdb=" N   PHE B  50 " --> pdb=" O   PHE B  46 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   MET B  59 " --> pdb=" O   LYS B  55 " (cutoff:3.500A)
      Proline residue:  B  60  - end of helix
      removed outlier: 3.673A  pdb=" N   ILE B  73 " --> pdb=" O   GLY B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 108
    Processing helix  chain 'B' and resid 131 through 137
      removed outlier: 3.846A  pdb=" N   ILE B 137 " --> pdb=" O   ILE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 149
    Processing helix  chain 'B' and resid 150 through 171
      removed outlier: 4.205A  pdb=" N   THR B 154 " --> pdb=" O   GLN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 220
      removed outlier: 3.690A  pdb=" N   TYR B 204 " --> pdb=" O   GLY B 200 " (cutoff:3.500A)
      Proline residue:  B 206  - end of helix
    Processing helix  chain 'B' and resid 223 through 255
      removed outlier: 3.694A  pdb=" N   GLU B 227 " --> pdb=" O   LYS B 223 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU B 228 " --> pdb=" O   VAL B 224 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS B 230 " --> pdb=" O   GLY B 226 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL B 231 " --> pdb=" O   GLU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 275
      removed outlier: 3.633A  pdb=" N   LYS B 264 " --> pdb=" O   SER B 260 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ASP B 267 " --> pdb=" O   LYS B 263 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ALA B 268 " --> pdb=" O   LYS B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 292
      removed outlier: 4.411A  pdb=" N   VAL B 284 " --> pdb=" O   GLY B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 310
      Proline residue:  B 304  - end of helix
      removed outlier: 3.748A  pdb=" N   THR B 308 " --> pdb=" O   PRO B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 330
    Processing helix  chain 'B' and resid 334 through 352
    Processing helix  chain 'B' and resid 357 through 371
      removed outlier: 4.147A  pdb=" N   ILE B 361 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   MET B 365 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 416
      removed outlier: 3.733A  pdb=" N   ILE B 389 " --> pdb=" O   MET B 385 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE B 392 " --> pdb=" O   GLY B 388 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   MET B 395 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY B 396 " --> pdb=" O   ILE B 392 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 32
      removed outlier: 3.544A  pdb=" N   HIS C  32 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 73
      removed outlier: 4.238A  pdb=" N   ALA C  38 " --> pdb=" O   GLY C  34 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   LYS C  40 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR C  41 " --> pdb=" O   ASP C  37 " (cutoff:3.500A)
      Proline residue:  C  45  - end of helix
      removed outlier: 3.826A  pdb=" N   PHE C  50 " --> pdb=" O   PHE C  46 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU C  53 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU C  57 " --> pdb=" O   LEU C  53 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET C  59 " --> pdb=" O   LYS C  55 " (cutoff:3.500A)
      Proline residue:  C  60  - end of helix
      removed outlier: 3.674A  pdb=" N   ILE C  73 " --> pdb=" O   GLY C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 108
    Processing helix  chain 'C' and resid 131 through 137
      removed outlier: 3.846A  pdb=" N   ILE C 137 " --> pdb=" O   ILE C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 149
    Processing helix  chain 'C' and resid 150 through 171
      removed outlier: 4.213A  pdb=" N   THR C 154 " --> pdb=" O   GLN C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 220
      removed outlier: 3.690A  pdb=" N   TYR C 204 " --> pdb=" O   GLY C 200 " (cutoff:3.500A)
      Proline residue:  C 206  - end of helix
    Processing helix  chain 'C' and resid 223 through 255
      removed outlier: 3.695A  pdb=" N   GLU C 227 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU C 228 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS C 230 " --> pdb=" O   GLY C 226 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   VAL C 231 " --> pdb=" O   GLU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 275
      removed outlier: 3.632A  pdb=" N   LYS C 264 " --> pdb=" O   SER C 260 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASP C 267 " --> pdb=" O   LYS C 263 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ALA C 268 " --> pdb=" O   LYS C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 292
      removed outlier: 4.411A  pdb=" N   VAL C 284 " --> pdb=" O   GLY C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 310
      Proline residue:  C 304  - end of helix
      removed outlier: 3.748A  pdb=" N   THR C 308 " --> pdb=" O   PRO C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 330
    Processing helix  chain 'C' and resid 334 through 352
    Processing helix  chain 'C' and resid 357 through 371
      removed outlier: 4.147A  pdb=" N   ILE C 361 " --> pdb=" O   GLY C 357 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   MET C 365 " --> pdb=" O   ILE C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 376 through 416
      removed outlier: 3.734A  pdb=" N   ILE C 389 " --> pdb=" O   MET C 385 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ALA C 391 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE C 392 " --> pdb=" O   GLY C 388 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY C 396 " --> pdb=" O   ILE C 392 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLU C 416 " --> pdb=" O   VAL C 412 " (cutoff:3.500A)

    774 hydrogen bonds defined for protein.
    2322 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: 1.47

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2721
        1.34 -     1.46: 1545
        1.46 -     1.57: 4623
        1.57 -     1.69: 0
        1.69 -     1.80: 102
  Bond restraints: 8991
  Sorted by residual:
  bond pdb=" N   ASN C 148 "
       pdb=" CA  ASN C 148 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.16e-02 7.43e+03 8.44e+00
  bond pdb=" N   ASN B 148 "
       pdb=" CA  ASN B 148 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.22e-02 6.72e+03 7.84e+00
  bond pdb=" CB  ILE B 187 "
       pdb=" CG2 ILE B 187 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.51e+00
  bond pdb=" CB  ILE A 187 "
       pdb=" CG2 ILE A 187 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.38e+00
  bond pdb=" CB  ILE C 187 "
       pdb=" CG2 ILE C 187 "
    ideal  model  delta    sigma   weight residual
    1.521  1.432  0.089 3.30e-02 9.18e+02 7.32e+00
  ... (remaining 8986 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 11036
        1.40 -     2.81: 965
        2.81 -     4.21: 184
        4.21 -     5.61: 36
        5.61 -     7.02: 13
  Bond angle restraints: 12234
  Sorted by residual:
  angle pdb=" C   GLN A 150 "
        pdb=" N   VAL A 151 "
        pdb=" CA  VAL A 151 "
      ideal   model   delta    sigma   weight residual
     120.72  127.63   -6.91 1.22e+00 6.72e-01 3.21e+01
  angle pdb=" C   GLN C 150 "
        pdb=" N   VAL C 151 "
        pdb=" CA  VAL C 151 "
      ideal   model   delta    sigma   weight residual
     120.72  127.52   -6.80 1.22e+00 6.72e-01 3.11e+01
  angle pdb=" C   GLN B 150 "
        pdb=" N   VAL B 151 "
        pdb=" CA  VAL B 151 "
      ideal   model   delta    sigma   weight residual
     120.72  127.50   -6.78 1.22e+00 6.72e-01 3.09e+01
  angle pdb=" N   GLN A 150 "
        pdb=" CA  GLN A 150 "
        pdb=" CB  GLN A 150 "
      ideal   model   delta    sigma   weight residual
     110.60  104.63    5.97 1.52e+00 4.33e-01 1.54e+01
  angle pdb=" N   GLN B 150 "
        pdb=" CA  GLN B 150 "
        pdb=" CB  GLN B 150 "
      ideal   model   delta    sigma   weight residual
     110.60  104.73    5.87 1.52e+00 4.33e-01 1.49e+01
  ... (remaining 12229 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.92: 4677
       11.92 -    23.85: 491
       23.85 -    35.77: 127
       35.77 -    47.70: 39
       47.70 -    59.62: 9
  Dihedral angle restraints: 5343
    sinusoidal: 1947
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CA  GLY B 221 "
           pdb=" C   GLY B 221 "
           pdb=" N   VAL B 222 "
           pdb=" CA  VAL B 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.89  -23.11     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  GLY A 221 "
           pdb=" C   GLY A 221 "
           pdb=" N   VAL A 222 "
           pdb=" CA  VAL A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  GLY C 221 "
           pdb=" C   GLY C 221 "
           pdb=" N   VAL C 222 "
           pdb=" CA  VAL C 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.96  -23.04     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 5340 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 910
       0.038 -    0.076: 434
       0.076 -    0.113: 170
       0.113 -    0.151: 37
       0.151 -    0.189: 9
  Chirality restraints: 1560
  Sorted by residual:
  chirality pdb=" CB  ILE C 160 "
            pdb=" CA  ILE C 160 "
            pdb=" CG1 ILE C 160 "
            pdb=" CG2 ILE C 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.91e-01
  chirality pdb=" CB  ILE A 160 "
            pdb=" CA  ILE A 160 "
            pdb=" CG1 ILE A 160 "
            pdb=" CG2 ILE A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CB  ILE B 160 "
            pdb=" CA  ILE B 160 "
            pdb=" CG1 ILE B 160 "
            pdb=" CG2 ILE B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.42e-01
  ... (remaining 1557 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B  59 "   -0.036 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO B  60 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B  60 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  60 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  59 "   -0.037 5.00e-02 4.00e+02   5.49e-02 4.82e+00
        pdb=" N   PRO A  60 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A  60 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  60 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C  59 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.80e+00
        pdb=" N   PRO C  60 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2002
        2.77 -     3.30: 9862
        3.30 -     3.83: 14305
        3.83 -     4.37: 15888
        4.37 -     4.90: 27150
  Nonbonded interactions: 69207
  Sorted by model distance:
  nonbonded pdb=" N   SER B 278 "
            pdb=" OXT ASP B 501 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" N   SER A 278 "
            pdb=" OXT ASP A 501 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" N   SER C 278 "
            pdb=" OXT ASP C 501 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   VAL C 355 "
            pdb=" N   ASP C 501 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   VAL A 355 "
            pdb=" N   ASP A 501 "
     model   vdw
     2.290 3.120
  ... (remaining 69202 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.620
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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      :  0.012   0.090   8991  Z= 0.495
  Angle     :  0.912   7.016  12234  Z= 0.533
  Chirality :  0.050   0.189   1560
  Planarity :  0.006   0.055   1488
  Dihedral  : 11.334  59.622   3183
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.21), residues: 1179
  helix: -0.76 (0.14), residues: 1008
  sheet:  None (None), residues: 0
  loop : -2.15 (0.38), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  52 
 TYR   0.035   0.003   TYR B 299 
 PHE   0.012   0.002   PHE B  63 
 HIS   0.003   0.002   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.01186 ( 8991)
  covalent geometry    : angle       0.91208 (12234)
  hydrogen bonds       : bond        0.16399 (  774)
  hydrogen bonds       : angle       7.18191 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 330
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.6862 (mmp-170) cc_final: 0.6609 (ttt180)
REVERT: A  244 LEU cc_start: 0.8950 (mt) cc_final: 0.8657 (mm)
REVERT: A  270 LEU cc_start: 0.8492 (mm) cc_final: 0.8226 (mt)
REVERT: A  311 MET cc_start: 0.8813 (mtm) cc_final: 0.8497 (mtp)
REVERT: A  385 MET cc_start: 0.8742 (mtt) cc_final: 0.8522 (mtp)
REVERT: B   85 ILE cc_start: 0.8482 (mm) cc_final: 0.8163 (tp)
REVERT: B  194 MET cc_start: 0.8766 (mmm) cc_final: 0.8210 (mmt)
REVERT: B  267 ASP cc_start: 0.8136 (t0) cc_final: 0.7792 (t0)
REVERT: B  311 MET cc_start: 0.8671 (mtm) cc_final: 0.8229 (mtp)
REVERT: B  385 MET cc_start: 0.8626 (mtt) cc_final: 0.8292 (mtp)
REVERT: C   77 ARG cc_start: 0.6939 (mmp-170) cc_final: 0.6533 (ttt180)
REVERT: C  405 ASP cc_start: 0.8073 (m-30) cc_final: 0.7815 (m-30)
REVERT: B  501 ASP cc_start: 0.7982 (m-30) cc_final: 0.7564 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 330
  average time/residue: 0.0713
  time to fit residues: 34.3946
Evaluate side-chains
  231 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 401 ASN ** 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 = 0.3754 r_free = 0.3754 target = 0.149616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109938 restraints weight = 14860.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.109390 restraints weight = 12070.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.110677 restraints weight = 9879.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.110952 restraints weight = 8775.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111110 restraints weight = 8021.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8991  Z= 0.190
  Angle     :  0.675  10.879  12234  Z= 0.361
  Chirality :  0.043   0.325   1560
  Planarity :  0.005   0.042   1488
  Dihedral  :  5.668  70.428   1263
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 11.08 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.24), residues: 1179
  helix:  1.18 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.33 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 397 
 TYR   0.026   0.002   TYR C 299 
 PHE   0.021   0.002   PHE C 248 
 HIS   0.001   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8991)
  covalent geometry    : angle       0.67488 (12234)
  hydrogen bonds       : bond        0.07287 (  774)
  hydrogen bonds       : angle       5.04263 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 283
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.6371 (mmp-170) cc_final: 0.5940 (ttt180)
REVERT: A   85 ILE cc_start: 0.8591 (mm) cc_final: 0.8312 (tp)
REVERT: A  248 PHE cc_start: 0.7831 (m-80) cc_final: 0.7398 (m-80)
REVERT: A  267 ASP cc_start: 0.7918 (t0) cc_final: 0.7673 (t0)
REVERT: A  369 SER cc_start: 0.9471 (t) cc_final: 0.9224 (p)
REVERT: A  395 MET cc_start: 0.6572 (mtm) cc_final: 0.6343 (mtm)
REVERT: B   85 ILE cc_start: 0.8501 (mm) cc_final: 0.8234 (tp)
REVERT: B  244 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8686 (mm)
REVERT: B  270 LEU cc_start: 0.8396 (mm) cc_final: 0.8173 (mt)
REVERT: B  287 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8440 (ttp-170)
REVERT: B  368 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: B  385 MET cc_start: 0.8620 (mtt) cc_final: 0.8418 (mtp)
REVERT: B  395 MET cc_start: 0.6214 (mtm) cc_final: 0.5833 (mtm)
REVERT: B  406 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (mm)
REVERT: C   40 LYS cc_start: 0.8685 (tttm) cc_final: 0.8373 (ttmt)
REVERT: C   77 ARG cc_start: 0.6390 (mmp-170) cc_final: 0.5924 (ttp-170)
REVERT: C   89 TYR cc_start: 0.8805 (m-10) cc_final: 0.8325 (m-10)
REVERT: C  244 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8749 (mm)
REVERT: C  369 SER cc_start: 0.9478 (t) cc_final: 0.9221 (p)
REVERT: C  385 MET cc_start: 0.8836 (mtm) cc_final: 0.8470 (mtp)
REVERT: C  399 MET cc_start: 0.8749 (tmm) cc_final: 0.7780 (tmm)
REVERT: C  405 ASP cc_start: 0.8132 (m-30) cc_final: 0.7872 (m-30)
  outliers start: 30
  outliers final: 20
  residues processed: 298
  average time/residue: 0.0699
  time to fit residues: 30.4938
Evaluate side-chains
  244 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  411 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  369 SER
Chi-restraints excluded: chain B residue  406 LEU
Chi-restraints excluded: chain C residue  244 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  366 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 93 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 401 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.147373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.107207 restraints weight = 14496.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108688 restraints weight = 11401.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.109797 restraints weight = 8274.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109615 restraints weight = 6914.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.109680 restraints weight = 6883.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8991  Z= 0.164
  Angle     :  0.661  11.323  12234  Z= 0.340
  Chirality :  0.043   0.302   1560
  Planarity :  0.004   0.038   1488
  Dihedral  :  5.779  82.733   1263
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 15.55 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.24), residues: 1179
  helix:  1.54 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.08 (0.45), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 397 
 TYR   0.019   0.001   TYR B  88 
 PHE   0.039   0.002   PHE C 248 
 HIS   0.001   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8991)
  covalent geometry    : angle       0.66134 (12234)
  hydrogen bonds       : bond        0.06345 (  774)
  hydrogen bonds       : angle       4.75082 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 241
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6193 (mmp-170) cc_final: 0.5863 (ttp-170)
REVERT: A   85 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (tp)
REVERT: A  287 ARG cc_start: 0.8646 (ttp-170) cc_final: 0.8435 (tmm160)
REVERT: A  369 SER cc_start: 0.9536 (t) cc_final: 0.9288 (p)
REVERT: A  403 THR cc_start: 0.9099 (m) cc_final: 0.8761 (p)
REVERT: B   11 PRO cc_start: 0.8156 (Cg_exo) cc_final: 0.7943 (Cg_endo)
REVERT: B   88 TYR cc_start: 0.8687 (t80) cc_final: 0.8128 (t80)
REVERT: B  406 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8560 (mm)
REVERT: C  244 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8758 (mm)
REVERT: C  385 MET cc_start: 0.8645 (mtm) cc_final: 0.8231 (mtp)
REVERT: C  409 THR cc_start: 0.9262 (m) cc_final: 0.9009 (t)
  outliers start: 36
  outliers final: 20
  residues processed: 253
  average time/residue: 0.0622
  time to fit residues: 24.1902
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 223
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  406 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  244 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  366 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 27 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   chunk 95 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.145275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.106783 restraints weight = 14528.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.106588 restraints weight = 12463.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.107917 restraints weight = 11443.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108013 restraints weight = 8871.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.108533 restraints weight = 9120.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8991  Z= 0.176
  Angle     :  0.688  13.778  12234  Z= 0.345
  Chirality :  0.044   0.360   1560
  Planarity :  0.004   0.037   1488
  Dihedral  :  5.930  89.645   1263
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 16.19 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.24), residues: 1179
  helix:  1.57 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.20 (0.45), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 287 
 TYR   0.018   0.001   TYR A 299 
 PHE   0.027   0.002   PHE C 324 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8991)
  covalent geometry    : angle       0.68841 (12234)
  hydrogen bonds       : bond        0.06354 (  774)
  hydrogen bonds       : angle       4.64058 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 232
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6305 (mmp-170) cc_final: 0.5819 (ttp-170)
REVERT: A  136 ASP cc_start: 0.8364 (t70) cc_final: 0.7984 (m-30)
REVERT: A  267 ASP cc_start: 0.8039 (t0) cc_final: 0.7831 (t0)
REVERT: A  287 ARG cc_start: 0.8780 (ttp-170) cc_final: 0.8395 (ttp-170)
REVERT: A  314 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9188 (t)
REVERT: A  369 SER cc_start: 0.9543 (t) cc_final: 0.9301 (p)
REVERT: B   85 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8359 (tp)
REVERT: B   88 TYR cc_start: 0.8713 (t80) cc_final: 0.8162 (t80)
REVERT: B  267 ASP cc_start: 0.7940 (t0) cc_final: 0.7477 (t0)
REVERT: B  406 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: C  248 PHE cc_start: 0.7604 (m-80) cc_final: 0.7211 (m-80)
REVERT: C  287 ARG cc_start: 0.8786 (ttp-170) cc_final: 0.8501 (ttp-170)
REVERT: C  385 MET cc_start: 0.8553 (mtm) cc_final: 0.8140 (mtp)
  outliers start: 53
  outliers final: 37
  residues processed: 251
  average time/residue: 0.0668
  time to fit residues: 25.4670
Evaluate side-chains
  257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 217
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  314 THR
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  411 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  102 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  406 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 101 optimal weight:    8.9990
   chunk 81 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0670
   chunk 102 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    0.7518

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.147543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108605 restraints weight = 14321.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.110116 restraints weight = 11481.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.110983 restraints weight = 9412.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.110915 restraints weight = 7472.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.111092 restraints weight = 7225.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8991  Z= 0.152
  Angle     :  0.656  14.913  12234  Z= 0.326
  Chirality :  0.043   0.281   1560
  Planarity :  0.004   0.037   1488
  Dihedral  :  5.792  84.762   1263
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.74 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.24), residues: 1179
  helix:  1.66 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -0.68 (0.46), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 397 
 TYR   0.027   0.001   TYR A  88 
 PHE   0.023   0.001   PHE C 324 
 HIS   0.002   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8991)
  covalent geometry    : angle       0.65573 (12234)
  hydrogen bonds       : bond        0.05674 (  774)
  hydrogen bonds       : angle       4.48825 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 240
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   30 LEU cc_start: 0.7649 (tt) cc_final: 0.7443 (tt)
REVERT: A   77 ARG cc_start: 0.6148 (mmp-170) cc_final: 0.5704 (ttp-170)
REVERT: A  369 SER cc_start: 0.9509 (t) cc_final: 0.9276 (p)
REVERT: A  403 THR cc_start: 0.9044 (m) cc_final: 0.8695 (p)
REVERT: B   85 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8333 (tp)
REVERT: B   88 TYR cc_start: 0.8677 (t80) cc_final: 0.8123 (t80)
REVERT: C  247 TYR cc_start: 0.7770 (m-80) cc_final: 0.7403 (m-80)
REVERT: C  267 ASP cc_start: 0.7791 (t0) cc_final: 0.7449 (t0)
REVERT: C  287 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8474 (ttp-170)
  outliers start: 31
  outliers final: 26
  residues processed: 252
  average time/residue: 0.0633
  time to fit residues: 24.2819
Evaluate side-chains
  256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 229
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  269 MET
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0370
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.147575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.108900 restraints weight = 14263.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.109295 restraints weight = 11475.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110183 restraints weight = 11410.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.110353 restraints weight = 8364.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.110433 restraints weight = 8499.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8991  Z= 0.144
  Angle     :  0.642  15.452  12234  Z= 0.323
  Chirality :  0.043   0.303   1560
  Planarity :  0.004   0.041   1488
  Dihedral  :  5.668  87.580   1263
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.91 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.24), residues: 1179
  helix:  1.60 (0.16), residues: 1041
  sheet:  None (None), residues: 0
  loop : -0.51 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.014   0.001   TYR A 299 
 PHE   0.024   0.001   PHE A 261 
 HIS   0.001   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8991)
  covalent geometry    : angle       0.64153 (12234)
  hydrogen bonds       : bond        0.05272 (  774)
  hydrogen bonds       : angle       4.40836 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 232
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.5984 (mmp-170) cc_final: 0.5587 (ttp-170)
REVERT: A  267 ASP cc_start: 0.7973 (t0) cc_final: 0.7443 (t0)
REVERT: A  287 ARG cc_start: 0.8762 (tmm160) cc_final: 0.8532 (ttp-170)
REVERT: A  403 THR cc_start: 0.9085 (m) cc_final: 0.8679 (p)
REVERT: B   85 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8187 (tp)
REVERT: B   88 TYR cc_start: 0.8645 (t80) cc_final: 0.8241 (t80)
REVERT: C   11 PRO cc_start: 0.7712 (Cg_exo) cc_final: 0.6772 (Cg_endo)
REVERT: C   14 GLN cc_start: 0.8761 (mp10) cc_final: 0.8051 (mp10)
REVERT: C  247 TYR cc_start: 0.7638 (m-80) cc_final: 0.7308 (m-80)
REVERT: C  267 ASP cc_start: 0.7887 (t0) cc_final: 0.7568 (t0)
REVERT: C  287 ARG cc_start: 0.8779 (ttp-170) cc_final: 0.8452 (ttp-170)
  outliers start: 36
  outliers final: 27
  residues processed: 245
  average time/residue: 0.0617
  time to fit residues: 23.3313
Evaluate side-chains
  239 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 103 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** 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 = 0.3701 r_free = 0.3701 target = 0.145384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.105984 restraints weight = 14371.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.106506 restraints weight = 12090.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107464 restraints weight = 11274.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107389 restraints weight = 8504.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107567 restraints weight = 9175.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8991  Z= 0.156
  Angle     :  0.662  16.289  12234  Z= 0.333
  Chirality :  0.042   0.169   1560
  Planarity :  0.004   0.039   1488
  Dihedral  :  5.394  85.413   1263
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.30 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.24), residues: 1179
  helix:  1.78 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -0.55 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 397 
 TYR   0.019   0.001   TYR A  88 
 PHE   0.024   0.001   PHE B 261 
 HIS   0.001   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8991)
  covalent geometry    : angle       0.66185 (12234)
  hydrogen bonds       : bond        0.05570 (  774)
  hydrogen bonds       : angle       4.40270 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 226
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6000 (mmp-170) cc_final: 0.5644 (ttp-170)
REVERT: A  403 THR cc_start: 0.9077 (m) cc_final: 0.8684 (p)
REVERT: B   85 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8196 (tp)
REVERT: B   88 TYR cc_start: 0.8656 (t80) cc_final: 0.8213 (t80)
REVERT: C   14 GLN cc_start: 0.8783 (mp10) cc_final: 0.8479 (mp10)
REVERT: C  247 TYR cc_start: 0.7658 (m-10) cc_final: 0.7270 (m-80)
REVERT: C  267 ASP cc_start: 0.7988 (t0) cc_final: 0.7626 (t0)
REVERT: C  269 MET cc_start: 0.5906 (ttp) cc_final: 0.5420 (mtp)
REVERT: C  287 ARG cc_start: 0.8804 (ttp-170) cc_final: 0.8514 (ttp-170)
  outliers start: 37
  outliers final: 30
  residues processed: 240
  average time/residue: 0.0659
  time to fit residues: 23.7095
Evaluate side-chains
  245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 214
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  411 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  202 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  365 MET
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 401 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.148875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.111365 restraints weight = 14212.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.110027 restraints weight = 13616.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.111468 restraints weight = 11646.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111706 restraints weight = 9013.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.111997 restraints weight = 8321.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.5081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   8991  Z= 0.149
  Angle     :  0.658  16.769  12234  Z= 0.331
  Chirality :  0.043   0.214   1560
  Planarity :  0.004   0.038   1488
  Dihedral  :  5.196  80.425   1263
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 21.30 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.24), residues: 1179
  helix:  1.72 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.56 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.022   0.001   TYR A  88 
 PHE   0.022   0.001   PHE B 261 
 HIS   0.001   0.000   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8991)
  covalent geometry    : angle       0.65793 (12234)
  hydrogen bonds       : bond        0.05265 (  774)
  hydrogen bonds       : angle       4.37963 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 229
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.5969 (mmp-170) cc_final: 0.5648 (ttp-170)
REVERT: A   89 TYR cc_start: 0.8812 (m-10) cc_final: 0.8179 (m-10)
REVERT: A  267 ASP cc_start: 0.7944 (t0) cc_final: 0.7659 (t0)
REVERT: A  287 ARG cc_start: 0.8763 (tmm160) cc_final: 0.8539 (ttp-170)
REVERT: A  403 THR cc_start: 0.9045 (m) cc_final: 0.8661 (p)
REVERT: B   85 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8175 (tp)
REVERT: B   88 TYR cc_start: 0.8609 (t80) cc_final: 0.8198 (t80)
REVERT: C  267 ASP cc_start: 0.8125 (t0) cc_final: 0.7769 (t0)
REVERT: C  287 ARG cc_start: 0.8740 (ttp-170) cc_final: 0.8485 (ttp-170)
REVERT: C  325 ILE cc_start: 0.8813 (mm) cc_final: 0.8538 (mt)
  outliers start: 39
  outliers final: 32
  residues processed: 245
  average time/residue: 0.0631
  time to fit residues: 23.3470
Evaluate side-chains
  249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 216
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  269 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  365 MET
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  239 LEU
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 3 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 105 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    1.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.146235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.108464 restraints weight = 14528.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.108358 restraints weight = 13072.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.109435 restraints weight = 12142.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.109397 restraints weight = 9244.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.109681 restraints weight = 8611.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.5056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   8991  Z= 0.173
  Angle     :  0.699  16.656  12234  Z= 0.349
  Chirality :  0.044   0.286   1560
  Planarity :  0.004   0.045   1488
  Dihedral  :  5.024  73.704   1263
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.73 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.24), residues: 1179
  helix:  1.69 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.56 (0.47), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 397 
 TYR   0.019   0.001   TYR C  88 
 PHE   0.020   0.001   PHE B 261 
 HIS   0.001   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8991)
  covalent geometry    : angle       0.69929 (12234)
  hydrogen bonds       : bond        0.05713 (  774)
  hydrogen bonds       : angle       4.43683 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.7848 (tt) cc_final: 0.7494 (pp)
REVERT: A   77 ARG cc_start: 0.6138 (mmp-170) cc_final: 0.5695 (ttp-170)
REVERT: A  169 MET cc_start: 0.8359 (tpp) cc_final: 0.8065 (mtt)
REVERT: A  385 MET cc_start: 0.8265 (mtp) cc_final: 0.7974 (ttp)
REVERT: A  403 THR cc_start: 0.9070 (m) cc_final: 0.8685 (p)
REVERT: B   85 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8208 (tp)
REVERT: B   88 TYR cc_start: 0.8634 (t80) cc_final: 0.8292 (t80)
REVERT: C  267 ASP cc_start: 0.7916 (t0) cc_final: 0.7611 (t0)
REVERT: C  287 ARG cc_start: 0.8797 (ttp-170) cc_final: 0.8553 (ttp-170)
REVERT: C  325 ILE cc_start: 0.8832 (mm) cc_final: 0.8629 (mt)
  outliers start: 38
  outliers final: 32
  residues processed: 233
  average time/residue: 0.0710
  time to fit residues: 25.0874
Evaluate side-chains
  245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 212
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  202 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  386 ILE
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 43 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.1982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.145639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.107213 restraints weight = 14432.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.108275 restraints weight = 11804.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109028 restraints weight = 11178.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.109204 restraints weight = 9104.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.109486 restraints weight = 9119.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8991  Z= 0.165
  Angle     :  0.699  16.544  12234  Z= 0.349
  Chirality :  0.044   0.308   1560
  Planarity :  0.004   0.043   1488
  Dihedral  :  4.827  66.460   1263
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.94 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.24), residues: 1179
  helix:  1.72 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.41 (0.47), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  77 
 TYR   0.022   0.001   TYR A  88 
 PHE   0.021   0.001   PHE B 261 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8991)
  covalent geometry    : angle       0.69938 (12234)
  hydrogen bonds       : bond        0.05792 (  774)
  hydrogen bonds       : angle       4.44203 ( 2322)

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

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

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2358 Ramachandran restraints generated.
    1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.7648 (tt) cc_final: 0.7409 (pp)
REVERT: A   77 ARG cc_start: 0.6095 (mmp-170) cc_final: 0.5667 (ttp-170)
REVERT: A  385 MET cc_start: 0.8308 (mtp) cc_final: 0.8010 (ttp)
REVERT: A  403 THR cc_start: 0.9087 (m) cc_final: 0.8700 (p)
REVERT: B   85 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8128 (tp)
REVERT: B   88 TYR cc_start: 0.8645 (t80) cc_final: 0.8354 (t80)
REVERT: B  202 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8117 (tpp)
REVERT: C  267 ASP cc_start: 0.7950 (t0) cc_final: 0.7619 (t0)
REVERT: C  287 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8602 (ttp-170)
REVERT: C  325 ILE cc_start: 0.8878 (mm) cc_final: 0.8607 (mt)
REVERT: C  372 LEU cc_start: 0.7540 (mp) cc_final: 0.7282 (tt)
  outliers start: 38
  outliers final: 33
  residues processed: 230
  average time/residue: 0.0665
  time to fit residues: 22.8845
Evaluate side-chains
  240 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  202 MET
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  314 THR
Chi-restraints excluded: chain B residue  334 THR
Chi-restraints excluded: chain B residue  335 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  303 LEU
Chi-restraints excluded: chain C residue  314 THR
Chi-restraints excluded: chain C residue  334 THR
Chi-restraints excluded: chain C residue  335 VAL
Chi-restraints excluded: chain C residue  355 VAL
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain C residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0070
   overall best weight:    0.6000

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

Flipped N/Q/H residues before XYZ refinement:
** B 401 ASN ** 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 = 0.3730 r_free = 0.3730 target = 0.148558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111268 restraints weight = 14183.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.111885 restraints weight = 11987.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.112785 restraints weight = 11652.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.112869 restraints weight = 8349.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.112994 restraints weight = 8612.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.5340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8991  Z= 0.146
  Angle     :  0.680  16.655  12234  Z= 0.338
  Chirality :  0.043   0.186   1560
  Planarity :  0.004   0.042   1488
  Dihedral  :  4.684  62.974   1263
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.86 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.24), residues: 1179
  helix:  1.73 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.49 (0.47), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 105 
 TYR   0.021   0.001   TYR A  88 
 PHE   0.019   0.001   PHE B 261 
 HIS   0.001   0.000   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8991)
  covalent geometry    : angle       0.67968 (12234)
  hydrogen bonds       : bond        0.05240 (  774)
  hydrogen bonds       : angle       4.37505 ( 2322)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1355.17 seconds
wall clock time: 24 minutes 4.18 seconds (1444.18 seconds total)