Starting phenix.real_space_refine
on Thu Mar 13 10:22:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wyl_21968/03_2025/6wyl_21968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wyl_21968/03_2025/6wyl_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_2025/6wyl_21968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2025/6wyl_21968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2025/6wyl_21968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wyl_21968/03_2025/6wyl_21968.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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:
    C, B
  Time building chain proxies: 5.59, per 1000 atoms: 0.63
  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: 2.53
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.88
  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: 2.68

  Time building geometry restraints manager: 2.93 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.390
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.470
-------------------------------------------------------------------------------
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= 0.788
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (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
 HIS   0.003   0.002   HIS A  32 
 PHE   0.012   0.002   PHE B  63 
 TYR   0.035   0.003   TYR B 299 
 ARG   0.007   0.001   ARG C  52 

*********************** 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  : 1.127 
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: 0.8812 (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: 0.1808
  time to fit residues: 85.1262
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  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 88 optimal weight:    8.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3751 r_free = 0.3751 target = 0.149165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.109116 restraints weight = 14470.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.109096 restraints weight = 10176.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.109664 restraints weight = 8292.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8991  Z= 0.244
  Angle     :  0.677  11.026  12234  Z= 0.364
  Chirality :  0.043   0.248   1560
  Planarity :  0.005   0.043   1488
  Dihedral  :  5.652  68.992   1263
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 11.50 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.24), residues: 1179
  helix:  1.13 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.31 (0.45), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 332 
 PHE   0.019   0.002   PHE C 248 
 TYR   0.026   0.002   TYR C 299 
 ARG   0.005   0.001   ARG C 397 

*********************** 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
  302 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 272
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ARG cc_start: 0.6404 (mmp-170) cc_final: 0.5963 (ttt180)
REVERT: A   85 ILE cc_start: 0.8593 (mm) cc_final: 0.8283 (tp)
REVERT: A  242 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8503 (tm-30)
REVERT: A  248 PHE cc_start: 0.7983 (m-80) cc_final: 0.7457 (m-80)
REVERT: A  267 ASP cc_start: 0.8087 (t0) cc_final: 0.7829 (t0)
REVERT: A  369 SER cc_start: 0.9472 (t) cc_final: 0.9204 (p)
REVERT: B   85 ILE cc_start: 0.8508 (mm) cc_final: 0.8225 (tp)
REVERT: B  244 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8680 (mm)
REVERT: B  270 LEU cc_start: 0.8402 (mm) cc_final: 0.8169 (mt)
REVERT: B  287 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8518 (ttp-170)
REVERT: B  368 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7590 (mm-30)
REVERT: B  385 MET cc_start: 0.8648 (mtt) cc_final: 0.8425 (mtp)
REVERT: B  405 ASP cc_start: 0.8270 (m-30) cc_final: 0.7998 (m-30)
REVERT: B  406 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8634 (mm)
REVERT: C   40 LYS cc_start: 0.8657 (tttm) cc_final: 0.8333 (ttmt)
REVERT: C   77 ARG cc_start: 0.6545 (mmp-170) cc_final: 0.6111 (ttp-170)
REVERT: C   85 ILE cc_start: 0.8666 (mm) cc_final: 0.8419 (tp)
REVERT: C  244 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8690 (mm)
REVERT: C  369 SER cc_start: 0.9466 (OUTLIER) cc_final: 0.9196 (p)
REVERT: C  385 MET cc_start: 0.8797 (mtm) cc_final: 0.8464 (mtp)
REVERT: C  399 MET cc_start: 0.8795 (tmm) cc_final: 0.7724 (tmm)
REVERT: C  405 ASP cc_start: 0.8193 (m-30) cc_final: 0.7854 (m-30)
  outliers start: 30
  outliers final: 19
  residues processed: 286
  average time/residue: 0.1746
  time to fit residues: 71.5684
Evaluate side-chains
  237 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 213
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  242 GLN
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  130 LEU
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
Chi-restraints excluded: chain C residue  369 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 54 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 98 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.146786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.106781 restraints weight = 14553.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.107946 restraints weight = 11718.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.108931 restraints weight = 8357.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8991  Z= 0.218
  Angle     :  0.658  10.906  12234  Z= 0.343
  Chirality :  0.044   0.241   1560
  Planarity :  0.004   0.040   1488
  Dihedral  :  5.709  79.681   1263
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 15.34 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.24), residues: 1179
  helix:  1.55 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.01 (0.46), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.020   0.002   PHE B 261 
 TYR   0.019   0.002   TYR B  88 
 ARG   0.003   0.000   ARG A 397 

*********************** 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
  280 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 239
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6325 (mmp-170) cc_final: 0.5873 (ttp-170)
REVERT: A   85 ILE cc_start: 0.8619 (mm) cc_final: 0.8368 (tp)
REVERT: A  242 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8330 (tm-30)
REVERT: A  247 TYR cc_start: 0.8272 (m-80) cc_final: 0.7797 (m-80)
REVERT: A  270 LEU cc_start: 0.8254 (mm) cc_final: 0.8028 (mt)
REVERT: A  369 SER cc_start: 0.9519 (t) cc_final: 0.9277 (p)
REVERT: A  403 THR cc_start: 0.8810 (m) cc_final: 0.8475 (p)
REVERT: B   85 ILE cc_start: 0.8767 (mm) cc_final: 0.8480 (tp)
REVERT: B   88 TYR cc_start: 0.8716 (t80) cc_final: 0.8066 (t80)
REVERT: B  103 MET cc_start: 0.8681 (tpp) cc_final: 0.8435 (tmm)
REVERT: B  369 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9211 (p)
REVERT: B  406 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8597 (mm)
REVERT: C   89 TYR cc_start: 0.8770 (m-10) cc_final: 0.8227 (m-10)
REVERT: C  244 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8756 (mm)
REVERT: C  248 PHE cc_start: 0.7704 (m-80) cc_final: 0.7281 (m-80)
REVERT: C  385 MET cc_start: 0.8662 (mtm) cc_final: 0.8263 (mtp)
REVERT: C  405 ASP cc_start: 0.8092 (m-30) cc_final: 0.7840 (m-30)
  outliers start: 41
  outliers final: 24
  residues processed: 252
  average time/residue: 0.1592
  time to fit residues: 59.3447
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  242 GLN
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 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  303 LEU
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  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  335 VAL
Chi-restraints excluded: chain C residue  341 ILE
Chi-restraints excluded: chain C residue  366 VAL
Chi-restraints excluded: chain A residue  501 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0980
   chunk 26 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3738 r_free = 0.3738 target = 0.148926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.110706 restraints weight = 14467.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.110382 restraints weight = 13099.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.111425 restraints weight = 10298.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8991  Z= 0.185
  Angle     :  0.672  16.051  12234  Z= 0.331
  Chirality :  0.043   0.349   1560
  Planarity :  0.004   0.038   1488
  Dihedral  :  5.674  84.256   1263
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 16.61 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.24), residues: 1179
  helix:  1.63 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.10 (0.45), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS A  32 
 PHE   0.020   0.001   PHE B 261 
 TYR   0.017   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A 397 

*********************** 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
  290 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 250
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6093 (mmp-170) cc_final: 0.5744 (ttp-170)
REVERT: A   85 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (tp)
REVERT: A  242 GLN cc_start: 0.8451 (tt0) cc_final: 0.8250 (tm-30)
REVERT: A  247 TYR cc_start: 0.8012 (m-80) cc_final: 0.7623 (m-80)
REVERT: A  369 SER cc_start: 0.9490 (t) cc_final: 0.9278 (p)
REVERT: A  399 MET cc_start: 0.8816 (tmm) cc_final: 0.8321 (tpt)
REVERT: A  403 THR cc_start: 0.8862 (m) cc_final: 0.8494 (p)
REVERT: B   85 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8578 (tp)
REVERT: B   88 TYR cc_start: 0.8661 (t80) cc_final: 0.8129 (t80)
REVERT: B  166 THR cc_start: 0.9032 (m) cc_final: 0.8797 (p)
REVERT: B  267 ASP cc_start: 0.7919 (t0) cc_final: 0.7425 (t0)
REVERT: B  406 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8626 (mm)
REVERT: C  385 MET cc_start: 0.8560 (mtm) cc_final: 0.8108 (mtp)
REVERT: C  405 ASP cc_start: 0.7957 (m-30) cc_final: 0.7746 (m-30)
REVERT: C  409 THR cc_start: 0.9210 (m) cc_final: 0.8906 (t)
  outliers start: 40
  outliers final: 27
  residues processed: 264
  average time/residue: 0.1561
  time to fit residues: 60.9485
Evaluate side-chains
  263 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 233
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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  303 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  314 THR
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  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  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   48 ASP
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  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  501 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   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 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.108893 restraints weight = 14342.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110023 restraints weight = 11954.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.110833 restraints weight = 9964.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8991  Z= 0.208
  Angle     :  0.667  14.929  12234  Z= 0.332
  Chirality :  0.043   0.301   1560
  Planarity :  0.004   0.054   1488
  Dihedral  :  5.797  89.703   1263
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.74 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.24), residues: 1179
  helix:  1.64 (0.16), residues: 1038
  sheet:  None (None), residues: 0
  loop : -1.00 (0.48), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  32 
 PHE   0.022   0.001   PHE A 261 
 TYR   0.030   0.001   TYR A  88 
 ARG   0.011   0.000   ARG B 397 

*********************** 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
  282 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 243
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6081 (mmp-170) cc_final: 0.5702 (ttp-170)
REVERT: A  247 TYR cc_start: 0.8074 (m-80) cc_final: 0.7609 (m-80)
REVERT: A  369 SER cc_start: 0.9505 (t) cc_final: 0.9286 (p)
REVERT: A  399 MET cc_start: 0.8784 (tmm) cc_final: 0.8162 (tpt)
REVERT: A  403 THR cc_start: 0.8832 (m) cc_final: 0.8274 (p)
REVERT: B   85 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8517 (tp)
REVERT: B   88 TYR cc_start: 0.8704 (t80) cc_final: 0.8125 (t80)
REVERT: C  248 PHE cc_start: 0.7778 (m-80) cc_final: 0.7371 (m-80)
REVERT: C  385 MET cc_start: 0.8480 (mtm) cc_final: 0.8042 (mtp)
REVERT: C  405 ASP cc_start: 0.7873 (m-30) cc_final: 0.7649 (m-30)
REVERT: C  409 THR cc_start: 0.9145 (m) cc_final: 0.8872 (t)
  outliers start: 39
  outliers final: 28
  residues processed: 258
  average time/residue: 0.1765
  time to fit residues: 66.5020
Evaluate side-chains
  259 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 230
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
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  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   48 ASP
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  209 VAL
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  366 VAL
Chi-restraints excluded: chain C residue  406 LEU
Chi-restraints excluded: chain C residue  501 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 75 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**
C 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.109148 restraints weight = 14310.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.109927 restraints weight = 11690.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.110732 restraints weight = 10255.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8991  Z= 0.208
  Angle     :  0.661  15.642  12234  Z= 0.331
  Chirality :  0.043   0.316   1560
  Planarity :  0.004   0.049   1488
  Dihedral  :  5.798  88.841   1263
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.60 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.24), residues: 1179
  helix:  1.62 (0.16), residues: 1041
  sheet:  None (None), residues: 0
  loop : -0.65 (0.49), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.022   0.001   PHE B 261 
 TYR   0.015   0.001   TYR A 299 
 ARG   0.001   0.000   ARG A 105 

*********************** 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
  276 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 236
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6062 (mmp-170) cc_final: 0.5570 (ttp-170)
REVERT: A   89 TYR cc_start: 0.8876 (m-10) cc_final: 0.8342 (m-10)
REVERT: A  247 TYR cc_start: 0.7956 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  369 SER cc_start: 0.9510 (t) cc_final: 0.9301 (p)
REVERT: A  399 MET cc_start: 0.8739 (tmm) cc_final: 0.8312 (tpt)
REVERT: B   85 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8540 (tp)
REVERT: B   88 TYR cc_start: 0.8659 (t80) cc_final: 0.8182 (t80)
REVERT: C   11 PRO cc_start: 0.7832 (Cg_exo) cc_final: 0.7311 (Cg_endo)
REVERT: C   14 GLN cc_start: 0.8782 (mp10) cc_final: 0.8559 (mp10)
REVERT: C   42 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7657 (m-80)
REVERT: C   85 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8453 (tp)
REVERT: C  409 THR cc_start: 0.9123 (m) cc_final: 0.8849 (t)
  outliers start: 40
  outliers final: 29
  residues processed: 253
  average time/residue: 0.1626
  time to fit residues: 60.6107
Evaluate side-chains
  254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 222
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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  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  334 THR
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  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  335 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  130 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  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 37 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 107 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3712 r_free = 0.3712 target = 0.146453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.107351 restraints weight = 14333.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.108302 restraints weight = 11974.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108936 restraints weight = 11267.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8991  Z= 0.202
  Angle     :  0.644  16.148  12234  Z= 0.325
  Chirality :  0.042   0.166   1560
  Planarity :  0.004   0.049   1488
  Dihedral  :  5.665  89.054   1263
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.87 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.24), residues: 1179
  helix:  1.74 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.71 (0.47), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.024   0.001   PHE B 261 
 TYR   0.022   0.001   TYR A  88 
 ARG   0.001   0.000   ARG C 397 

*********************** 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
  264 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6012 (mmp-170) cc_final: 0.5623 (ttp-170)
REVERT: A  247 TYR cc_start: 0.8309 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  399 MET cc_start: 0.8745 (tmm) cc_final: 0.8217 (tpt)
REVERT: B   88 TYR cc_start: 0.8660 (t80) cc_final: 0.8230 (t80)
REVERT: C   11 PRO cc_start: 0.7977 (Cg_exo) cc_final: 0.7611 (Cg_endo)
REVERT: C   42 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7612 (m-80)
REVERT: C   85 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8413 (tp)
  outliers start: 38
  outliers final: 30
  residues processed: 243
  average time/residue: 0.1624
  time to fit residues: 58.1405
Evaluate side-chains
  247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 215
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  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  130 LEU
Chi-restraints excluded: chain B residue  202 MET
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  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  130 LEU
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  209 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  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 109 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.148486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.110735 restraints weight = 14606.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.110137 restraints weight = 14691.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.111229 restraints weight = 13489.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   8991  Z= 0.223
  Angle     :  0.678  16.764  12234  Z= 0.336
  Chirality :  0.043   0.305   1560
  Planarity :  0.004   0.045   1488
  Dihedral  :  5.468  86.212   1263
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.62 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.24), residues: 1179
  helix:  1.70 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.65 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C 332 
 PHE   0.023   0.001   PHE B 261 
 TYR   0.013   0.001   TYR A 299 
 ARG   0.003   0.000   ARG B 397 

*********************** 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
  256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 219
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.5995 (mmp-170) cc_final: 0.5682 (ttp-170)
REVERT: A  136 ASP cc_start: 0.8257 (t0) cc_final: 0.8022 (m-30)
REVERT: A  247 TYR cc_start: 0.8359 (m-80) cc_final: 0.8044 (m-80)
REVERT: A  399 MET cc_start: 0.8729 (tmm) cc_final: 0.8192 (tpt)
REVERT: B   88 TYR cc_start: 0.8596 (t80) cc_final: 0.8314 (t80)
REVERT: B  160 ILE cc_start: 0.9055 (mm) cc_final: 0.8494 (tt)
REVERT: C   11 PRO cc_start: 0.7788 (Cg_exo) cc_final: 0.7562 (Cg_endo)
REVERT: C   42 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7701 (m-80)
REVERT: C   85 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8432 (tp)
REVERT: C  325 ILE cc_start: 0.8794 (mm) cc_final: 0.8535 (mt)
  outliers start: 37
  outliers final: 31
  residues processed: 236
  average time/residue: 0.1524
  time to fit residues: 53.6200
Evaluate side-chains
  239 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 206
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  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  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 A residue  411 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  130 LEU
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  366 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   42 TYR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  101 ILE
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  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 12 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3731 r_free = 0.3731 target = 0.148504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.110662 restraints weight = 14568.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110486 restraints weight = 13640.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.112279 restraints weight = 11497.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8991  Z= 0.219
  Angle     :  0.678  16.748  12234  Z= 0.336
  Chirality :  0.043   0.289   1560
  Planarity :  0.004   0.043   1488
  Dihedral  :  5.215  81.458   1263
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.83 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.24), residues: 1179
  helix:  1.70 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.69 (0.46), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.023   0.001   PHE B 261 
 TYR   0.026   0.001   TYR A  88 
 ARG   0.005   0.000   ARG B 397 

*********************** 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
  262 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 224
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6041 (mmp-170) cc_final: 0.5625 (ttp-170)
REVERT: A  194 MET cc_start: 0.8953 (mmm) cc_final: 0.8750 (mmt)
REVERT: A  247 TYR cc_start: 0.8353 (m-80) cc_final: 0.8013 (m-80)
REVERT: A  385 MET cc_start: 0.8214 (mtp) cc_final: 0.7944 (ttp)
REVERT: B   88 TYR cc_start: 0.8608 (t80) cc_final: 0.8288 (t80)
REVERT: B  160 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8550 (tt)
REVERT: C   11 PRO cc_start: 0.7822 (Cg_exo) cc_final: 0.7598 (Cg_endo)
REVERT: C   42 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7644 (m-80)
REVERT: C   85 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8413 (tp)
REVERT: C  325 ILE cc_start: 0.8781 (mm) cc_final: 0.8523 (mt)
  outliers start: 38
  outliers final: 32
  residues processed: 239
  average time/residue: 0.1560
  time to fit residues: 55.3144
Evaluate side-chains
  246 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 211
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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  160 ILE
Chi-restraints excluded: chain A residue  303 LEU
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  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  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   42 TYR
Chi-restraints excluded: chain C residue   85 ILE
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  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 36 optimal weight:    0.0470
   chunk 76 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0770
   chunk 29 optimal weight:    0.9980
   chunk 109 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.5636

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.149930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.112341 restraints weight = 14436.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.113385 restraints weight = 12717.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.114132 restraints weight = 11891.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8991  Z= 0.201
  Angle     :  0.707  16.784  12234  Z= 0.344
  Chirality :  0.043   0.192   1560
  Planarity :  0.004   0.041   1488
  Dihedral  :  5.070  78.363   1263
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.32 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.24), residues: 1179
  helix:  1.72 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.65 (0.46), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 332 
 PHE   0.024   0.001   PHE A 324 
 TYR   0.024   0.001   TYR A  88 
 ARG   0.003   0.000   ARG B  77 

********************** 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
  256 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 224
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A   77 ARG cc_start: 0.6039 (mmp-170) cc_final: 0.5608 (ttp-170)
REVERT: A  194 MET cc_start: 0.8912 (mmm) cc_final: 0.8689 (mmt)
REVERT: A  247 TYR cc_start: 0.8344 (m-80) cc_final: 0.8040 (m-80)
REVERT: A  403 THR cc_start: 0.8924 (m) cc_final: 0.8613 (p)
REVERT: B   11 PRO cc_start: 0.8121 (Cg_exo) cc_final: 0.7877 (Cg_endo)
REVERT: B   88 TYR cc_start: 0.8612 (t80) cc_final: 0.8249 (t80)
REVERT: B  160 ILE cc_start: 0.8938 (mm) cc_final: 0.8611 (tt)
REVERT: C   11 PRO cc_start: 0.7812 (Cg_exo) cc_final: 0.7572 (Cg_endo)
REVERT: C   42 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7640 (m-80)
REVERT: C  325 ILE cc_start: 0.8786 (mm) cc_final: 0.8546 (mt)
  outliers start: 32
  outliers final: 25
  residues processed: 238
  average time/residue: 0.1627
  time to fit residues: 56.4634
Evaluate side-chains
  242 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
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  303 LEU
Chi-restraints excluded: chain A residue  311 MET
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  130 LEU
Chi-restraints excluded: chain B residue  303 LEU
Chi-restraints excluded: chain B residue  312 ASP
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   42 TYR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  107 PHE
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  335 VAL
Chi-restraints excluded: chain C residue  355 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 59 optimal weight:    0.1980
   chunk 28 optimal weight:    0.7980
   chunk 88 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 94 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.149897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.112125 restraints weight = 14396.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111883 restraints weight = 13695.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.113848 restraints weight = 11559.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8991  Z= 0.200
  Angle     :  0.690  16.730  12234  Z= 0.339
  Chirality :  0.043   0.175   1560
  Planarity :  0.004   0.041   1488
  Dihedral  :  4.888  74.688   1263
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 23.43 %
    Favored  : 73.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.24), residues: 1179
  helix:  1.73 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.61 (0.46), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 332 
 PHE   0.023   0.001   PHE A 324 
 TYR   0.023   0.001   TYR A  88 
 ARG   0.005   0.000   ARG B 397 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2645.64 seconds
wall clock time: 46 minutes 37.52 seconds (2797.52 seconds total)