Starting phenix.real_space_refine
on Fri Feb 14 03:35:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.39
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x16_21990/02_2025/6x16_21990.cif"
  }
  resolution = 3.39
  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=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      54      5.16       5
     C    6222      2.51       5
     N    1503      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9438
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3087
          Classifications: {'peptide': 416}
          Link IDs: {'PTRANS': 18, 'TRANS': 397}
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'6OU': 1, 'TB1': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.01, per 1000 atoms: 0.64
  Number of scatterers: 9438
  At special positions: 0
  Unit cell: (110.545, 109.472, 74.0543, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       3     15.00
     O    1656      8.00
     N    1503      7.00
     C    6222      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: 2.61
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2238

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      82.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 10
    Processing helix  chain 'B' and resid 11 through 33
      removed outlier: 3.569A  pdb=" N   LYS B  15 " --> pdb=" O   PRO B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 57
      Proline residue:  B  45  - end of helix
    Processing helix  chain 'B' and resid 57 through 74
      removed outlier: 4.006A  pdb=" N   ILE B  61 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 107
      removed outlier: 3.600A  pdb=" N   VAL B  83 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR B  88 " --> pdb=" O   LYS B  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 137
    Processing helix  chain 'B' and resid 141 through 148
      removed outlier: 3.513A  pdb=" N   ASN B 148 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 169
    Processing helix  chain 'B' and resid 174 through 220
      Proline residue:  B 206  - end of helix
    Processing helix  chain 'B' and resid 222 through 254
      removed outlier: 4.232A  pdb=" N   GLY B 226 " --> pdb=" O   VAL B 222 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 265
    Processing helix  chain 'B' and resid 265 through 275
      removed outlier: 3.778A  pdb=" N   ALA B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 295 through 300
    Processing helix  chain 'B' and resid 301 through 310
      removed outlier: 3.653A  pdb=" N   LEU B 305 " --> pdb=" O   PHE B 301 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   THR B 308 " --> pdb=" O   PRO B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 328
      removed outlier: 3.586A  pdb=" N   LEU B 316 " --> pdb=" O   ASP B 312 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   PHE B 323 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B 326 " --> pdb=" O   THR B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 347
      removed outlier: 3.521A  pdb=" N   ILE B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 371
      removed outlier: 3.677A  pdb=" N   CYS B 364 " --> pdb=" O   ALA B 360 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLY B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 388
      removed outlier: 3.648A  pdb=" N   ALA B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 414
      removed outlier: 3.943A  pdb=" N   MET B 395 " --> pdb=" O   ALA B 391 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   GLY B 396 " --> pdb=" O   ILE B 392 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   MET B 399 " --> pdb=" O   MET B 395 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B 400 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN B 401 " --> pdb=" O   ARG B 397 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 406 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3 through 10
    Processing helix  chain 'A' and resid 11 through 33
      removed outlier: 3.569A  pdb=" N   LYS A  15 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 57
      Proline residue:  A  45  - end of helix
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 4.006A  pdb=" N   ILE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 107
      removed outlier: 3.600A  pdb=" N   VAL A  83 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 137
    Processing helix  chain 'A' and resid 141 through 148
      removed outlier: 3.513A  pdb=" N   ASN A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 169
    Processing helix  chain 'A' and resid 174 through 220
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 222 through 254
      removed outlier: 4.232A  pdb=" N   GLY A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 265
    Processing helix  chain 'A' and resid 265 through 275
      removed outlier: 3.778A  pdb=" N   ALA A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 3.653A  pdb=" N   LEU A 305 " --> pdb=" O   PHE A 301 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 328
      removed outlier: 3.586A  pdb=" N   LEU A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   PHE A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 326 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 347
      removed outlier: 3.521A  pdb=" N   ILE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
      removed outlier: 3.677A  pdb=" N   CYS A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 388
      removed outlier: 3.648A  pdb=" N   ALA A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 414
      removed outlier: 3.943A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 5.001A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASN A 401 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASP A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 10
    Processing helix  chain 'C' and resid 11 through 33
      removed outlier: 3.569A  pdb=" N   LYS C  15 " --> pdb=" O   PRO C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 57
      Proline residue:  C  45  - end of helix
    Processing helix  chain 'C' and resid 57 through 74
      removed outlier: 4.005A  pdb=" N   ILE C  61 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 107
      removed outlier: 3.599A  pdb=" N   VAL C  83 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   TYR C  88 " --> pdb=" O   LYS C  84 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   PHE C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 137
    Processing helix  chain 'C' and resid 141 through 148
      removed outlier: 3.513A  pdb=" N   ASN C 148 " --> pdb=" O   GLY C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 169
    Processing helix  chain 'C' and resid 174 through 220
      Proline residue:  C 206  - end of helix
    Processing helix  chain 'C' and resid 222 through 254
      removed outlier: 4.232A  pdb=" N   GLY C 226 " --> pdb=" O   VAL C 222 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLU C 227 " --> pdb=" O   HIS C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 257 through 265
    Processing helix  chain 'C' and resid 265 through 275
      removed outlier: 3.778A  pdb=" N   ALA C 272 " --> pdb=" O   ALA C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 281 through 291
    Processing helix  chain 'C' and resid 295 through 300
    Processing helix  chain 'C' and resid 301 through 310
      removed outlier: 3.652A  pdb=" N   LEU C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   THR C 308 " --> pdb=" O   PRO C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 312 through 328
      removed outlier: 3.586A  pdb=" N   LEU C 316 " --> pdb=" O   ASP C 312 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   PHE C 323 " --> pdb=" O   GLY C 319 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA C 326 " --> pdb=" O   THR C 322 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 347
      removed outlier: 3.521A  pdb=" N   ILE C 341 " --> pdb=" O   GLN C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 371
      removed outlier: 3.676A  pdb=" N   CYS C 364 " --> pdb=" O   ALA C 360 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   SER C 369 " --> pdb=" O   MET C 365 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY C 371 " --> pdb=" O   LEU C 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 388
      removed outlier: 3.648A  pdb=" N   ALA C 384 " --> pdb=" O   ALA C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 414
      removed outlier: 3.943A  pdb=" N   MET C 395 " --> pdb=" O   ALA C 391 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   GLY C 396 " --> pdb=" O   ILE C 392 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   MET C 399 " --> pdb=" O   MET C 395 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL C 400 " --> pdb=" O   GLY C 396 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASN C 401 " --> pdb=" O   ARG C 397 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ASP C 405 " --> pdb=" O   ASN C 401 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU C 406 " --> pdb=" O   VAL C 402 " (cutoff:3.500A)

    694 hydrogen bonds defined for protein.
    2082 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: 2.69

  Time building geometry restraints manager: 2.98 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1455
        1.31 -     1.43: 2347
        1.43 -     1.56: 5669
        1.56 -     1.68: 45
        1.68 -     1.80: 102
  Bond restraints: 9618
  Sorted by residual:
  bond pdb=" C16 6OU A 501 "
       pdb=" O18 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.414 -0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" C16 6OU C 501 "
       pdb=" O18 6OU C 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.413 -0.086 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C16 6OU B 501 "
       pdb=" O18 6OU B 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.413 -0.086 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C31 6OU B 501 "
       pdb=" O30 6OU B 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.408 -0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" C31 6OU C 501 "
       pdb=" O30 6OU C 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.408 -0.077 2.00e-02 2.50e+03 1.48e+01
  ... (remaining 9613 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.11: 12844
        3.11 -     6.22: 191
        6.22 -     9.34: 39
        9.34 -    12.45: 6
       12.45 -    15.56: 3
  Bond angle restraints: 13083
  Sorted by residual:
  angle pdb=" O22 6OU C 501 "
        pdb=" P23 6OU C 501 "
        pdb=" O26 6OU C 501 "
      ideal   model   delta    sigma   weight residual
      93.95  109.51  -15.56 3.00e+00 1.11e-01 2.69e+01
  angle pdb=" O22 6OU B 501 "
        pdb=" P23 6OU B 501 "
        pdb=" O26 6OU B 501 "
      ideal   model   delta    sigma   weight residual
      93.95  109.49  -15.54 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" O22 6OU A 501 "
        pdb=" P23 6OU A 501 "
        pdb=" O26 6OU A 501 "
      ideal   model   delta    sigma   weight residual
      93.95  109.49  -15.54 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" N   ALA A 205 "
        pdb=" CA  ALA A 205 "
        pdb=" C   ALA A 205 "
      ideal   model   delta    sigma   weight residual
     109.81  121.12  -11.31 2.21e+00 2.05e-01 2.62e+01
  angle pdb=" N   ALA B 205 "
        pdb=" CA  ALA B 205 "
        pdb=" C   ALA B 205 "
      ideal   model   delta    sigma   weight residual
     109.81  121.07  -11.26 2.21e+00 2.05e-01 2.59e+01
  ... (remaining 13078 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.70: 5222
       21.70 -    43.39: 409
       43.39 -    65.08: 45
       65.08 -    86.78: 24
       86.78 -   108.47: 3
  Dihedral angle restraints: 5703
    sinusoidal: 2166
      harmonic: 3537
  Sorted by residual:
  dihedral pdb=" CA  VAL B  58 "
           pdb=" C   VAL B  58 "
           pdb=" N   MET B  59 "
           pdb=" CA  MET B  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.87  -19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  VAL C  58 "
           pdb=" C   VAL C  58 "
           pdb=" N   MET C  59 "
           pdb=" CA  MET C  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.90  -19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  VAL A  58 "
           pdb=" C   VAL A  58 "
           pdb=" N   MET A  59 "
           pdb=" CA  MET A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.91  -19.09     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5700 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1093
       0.039 -    0.079: 378
       0.079 -    0.118: 99
       0.118 -    0.157: 32
       0.157 -    0.196: 18
  Chirality restraints: 1620
  Sorted by residual:
  chirality pdb=" C20 6OU C 501 "
            pdb=" C19 6OU C 501 "
            pdb=" C21 6OU C 501 "
            pdb=" O30 6OU C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.54   -0.20 2.00e-01 2.50e+01 9.63e-01
  chirality pdb=" C20 6OU B 501 "
            pdb=" C19 6OU B 501 "
            pdb=" C21 6OU B 501 "
            pdb=" O30 6OU B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.54   -0.19 2.00e-01 2.50e+01 9.24e-01
  chirality pdb=" C20 6OU A 501 "
            pdb=" C19 6OU A 501 "
            pdb=" C21 6OU A 501 "
            pdb=" O30 6OU A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.54   -0.19 2.00e-01 2.50e+01 9.11e-01
  ... (remaining 1617 not shown)

  Planarity restraints: 1605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  44 "    0.045 5.00e-02 4.00e+02   6.68e-02 7.13e+00
        pdb=" N   PRO A  45 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  44 "   -0.045 5.00e-02 4.00e+02   6.67e-02 7.13e+00
        pdb=" N   PRO C  45 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  45 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C  45 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  44 "    0.045 5.00e-02 4.00e+02   6.67e-02 7.12e+00
        pdb=" N   PRO B  45 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1602 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 3012
        2.84 -     3.35: 8922
        3.35 -     3.87: 15515
        3.87 -     4.38: 17713
        4.38 -     4.90: 31435
  Nonbonded interactions: 76597
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  65 "
            pdb=" OH  TYR A 195 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG  SER C  65 "
            pdb=" OH  TYR C 195 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG  SER B  65 "
            pdb=" OH  TYR B 195 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG  SER C 278 "
            pdb=" O3  TB1 C 502 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER B 278 "
            pdb=" O3  TB1 B 502 "
     model   vdw
     2.323 3.040
  ... (remaining 76592 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
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      :  0.006   0.087   9618  Z= 0.423
  Angle     :  0.994  15.560  13083  Z= 0.481
  Chirality :  0.047   0.196   1620
  Planarity :  0.008   0.067   1605
  Dihedral  : 15.988 108.475   3465
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  7.72 %
    Favored  : 91.98 %
  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: -3.86 (0.18), residues: 1242
  helix: -2.31 (0.12), residues: 1005
  sheet:  None (None), residues: 0
  loop : -2.56 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS A  40 
 PHE   0.013   0.001   PHE A 107 
 TYR   0.018   0.001   TYR C 299 
 ARG   0.002   0.000   ARG B 105 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.868 
Fit side-chains
REVERT: B   59 MET cc_start: 0.7758 (mmm) cc_final: 0.7439 (mmp)
REVERT: B  169 MET cc_start: 0.8197 (mtm) cc_final: 0.7929 (mtm)
REVERT: B  217 MET cc_start: 0.7451 (mmt) cc_final: 0.6728 (mmt)
REVERT: B  269 MET cc_start: 0.7008 (mtm) cc_final: 0.6758 (mtp)
REVERT: B  310 ASN cc_start: 0.9366 (t0) cc_final: 0.9056 (t0)
REVERT: B  395 MET cc_start: 0.8527 (mtm) cc_final: 0.8250 (mtp)
REVERT: B  399 MET cc_start: 0.7310 (ttp) cc_final: 0.7054 (ttp)
REVERT: A  194 MET cc_start: 0.8359 (mmp) cc_final: 0.7952 (mmp)
REVERT: A  269 MET cc_start: 0.7102 (mtm) cc_final: 0.6819 (mtp)
REVERT: A  286 MET cc_start: 0.7002 (mtt) cc_final: 0.6524 (mtp)
REVERT: A  310 ASN cc_start: 0.9398 (t0) cc_final: 0.9000 (t0)
REVERT: A  399 MET cc_start: 0.7646 (ttp) cc_final: 0.7361 (ttp)
REVERT: C  217 MET cc_start: 0.7178 (mmt) cc_final: 0.6951 (mmt)
REVERT: C  269 MET cc_start: 0.7273 (mtm) cc_final: 0.6993 (mtp)
REVERT: C  399 MET cc_start: 0.7319 (ttp) cc_final: 0.6989 (ttp)
  outliers start: 3
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1667
  time to fit residues: 21.5046
Evaluate side-chains
  74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0270
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 111 optimal weight:    0.0370
   overall best weight:    0.2074

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

Flipped N/Q/H residues before XYZ refinement:
B  14 GLN
B 132 HIS
** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  14 GLN
A 132 HIS
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  14 GLN
C 132 HIS
C 318 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.144325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.112050 restraints weight = 11089.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.24
r_work: 0.2980 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9618  Z= 0.144
  Angle     :  0.521   7.945  13083  Z= 0.266
  Chirality :  0.036   0.118   1620
  Planarity :  0.006   0.053   1605
  Dihedral  : 12.088  96.685   1488
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.57 %
    Favored  : 89.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.23), residues: 1242
  helix: -0.22 (0.16), residues: 1017
  sheet:  None (None), residues: 0
  loop : -1.87 (0.35), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  40 
 PHE   0.005   0.000   PHE A  50 
 TYR   0.008   0.001   TYR C 299 
 ARG   0.002   0.000   ARG A 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: B  202 MET cc_start: 0.7725 (mmm) cc_final: 0.7440 (mmm)
REVERT: B  269 MET cc_start: 0.7100 (mtm) cc_final: 0.6881 (mtp)
REVERT: B  310 ASN cc_start: 0.9054 (t0) cc_final: 0.8841 (t0)
REVERT: B  395 MET cc_start: 0.8509 (mtm) cc_final: 0.8263 (mtp)
REVERT: A  269 MET cc_start: 0.7179 (mtm) cc_final: 0.6855 (mtp)
REVERT: A  310 ASN cc_start: 0.9137 (t0) cc_final: 0.8803 (t0)
REVERT: A  399 MET cc_start: 0.7582 (ttp) cc_final: 0.7307 (ttp)
REVERT: C   57 LEU cc_start: 0.8333 (mt) cc_final: 0.8107 (mt)
REVERT: C  217 MET cc_start: 0.7039 (mmt) cc_final: 0.6760 (mmt)
REVERT: C  269 MET cc_start: 0.6934 (mtm) cc_final: 0.6626 (mtp)
REVERT: C  311 MET cc_start: 0.8892 (mmt) cc_final: 0.8443 (mmt)
REVERT: C  399 MET cc_start: 0.7303 (ttp) cc_final: 0.6980 (ttp)
  outliers start: 10
  outliers final: 7
  residues processed: 84
  average time/residue: 0.1699
  time to fit residues: 22.5816
Evaluate side-chains
  83 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 113 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 89 optimal weight:    0.6980
   chunk 54 optimal weight:    0.1980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.140257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.107392 restraints weight = 11157.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.23
r_work: 0.2920 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9618  Z= 0.173
  Angle     :  0.523   7.856  13083  Z= 0.263
  Chirality :  0.036   0.118   1620
  Planarity :  0.005   0.053   1605
  Dihedral  : 10.899  94.680   1488
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.04 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.24), residues: 1242
  helix:  0.52 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -1.52 (0.37), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  40 
 PHE   0.006   0.001   PHE A  50 
 TYR   0.006   0.001   TYR A 299 
 ARG   0.001   0.000   ARG A 276 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.857 
Fit side-chains
REVERT: B  269 MET cc_start: 0.7048 (mtm) cc_final: 0.6799 (mtp)
REVERT: B  310 ASN cc_start: 0.9222 (t0) cc_final: 0.8822 (t0)
REVERT: B  311 MET cc_start: 0.8864 (mmt) cc_final: 0.7797 (mmt)
REVERT: B  395 MET cc_start: 0.8501 (mtm) cc_final: 0.8277 (mtp)
REVERT: A  194 MET cc_start: 0.8653 (mmp) cc_final: 0.8285 (mmp)
REVERT: A  269 MET cc_start: 0.7172 (mtm) cc_final: 0.6819 (mtp)
REVERT: A  310 ASN cc_start: 0.9261 (t0) cc_final: 0.8900 (t0)
REVERT: A  399 MET cc_start: 0.7671 (ttp) cc_final: 0.7435 (ttp)
REVERT: C  269 MET cc_start: 0.7027 (mtm) cc_final: 0.6684 (mtp)
REVERT: C  311 MET cc_start: 0.8856 (mmt) cc_final: 0.8565 (mmt)
REVERT: C  399 MET cc_start: 0.7394 (ttp) cc_final: 0.7100 (ttp)
  outliers start: 10
  outliers final: 8
  residues processed: 85
  average time/residue: 0.1671
  time to fit residues: 22.2975
Evaluate side-chains
  87 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.139573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.107548 restraints weight = 11010.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.07
r_work: 0.2902 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9618  Z= 0.189
  Angle     :  0.523   7.785  13083  Z= 0.263
  Chirality :  0.037   0.121   1620
  Planarity :  0.005   0.053   1605
  Dihedral  : 10.871  94.453   1488
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.35 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.24), residues: 1242
  helix:  0.84 (0.17), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.27 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.005   0.001   TYR A 236 
 ARG   0.001   0.000   ARG C 276 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.921 
Fit side-chains
REVERT: B  269 MET cc_start: 0.7244 (mtm) cc_final: 0.6986 (mtp)
REVERT: B  310 ASN cc_start: 0.9264 (t0) cc_final: 0.8911 (t0)
REVERT: B  311 MET cc_start: 0.8844 (mmt) cc_final: 0.8104 (mmt)
REVERT: B  395 MET cc_start: 0.8565 (mtm) cc_final: 0.8349 (mtp)
REVERT: A  194 MET cc_start: 0.8720 (mmp) cc_final: 0.8393 (mmp)
REVERT: A  399 MET cc_start: 0.7961 (ttp) cc_final: 0.7331 (ttp)
REVERT: C  311 MET cc_start: 0.8837 (mmt) cc_final: 0.8480 (mmt)
REVERT: C  399 MET cc_start: 0.7544 (ttp) cc_final: 0.6950 (ttp)
  outliers start: 12
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1714
  time to fit residues: 24.5450
Evaluate side-chains
  94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 88 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.137986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.105880 restraints weight = 11092.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.07
r_work: 0.2881 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9618  Z= 0.207
  Angle     :  0.531   7.783  13083  Z= 0.267
  Chirality :  0.037   0.121   1620
  Planarity :  0.005   0.053   1605
  Dihedral  : 10.840  94.338   1488
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.76 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1242
  helix:  0.98 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.94 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  40 
 PHE   0.006   0.001   PHE C  50 
 TYR   0.008   0.001   TYR B 254 
 ARG   0.001   0.000   ARG C 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.970 
Fit side-chains
REVERT: B  269 MET cc_start: 0.7215 (mtm) cc_final: 0.6946 (mtp)
REVERT: B  310 ASN cc_start: 0.9317 (t0) cc_final: 0.8923 (t0)
REVERT: B  395 MET cc_start: 0.8572 (mtm) cc_final: 0.8355 (mtp)
REVERT: A  269 MET cc_start: 0.7604 (mtm) cc_final: 0.7127 (mtp)
REVERT: A  399 MET cc_start: 0.7915 (ttp) cc_final: 0.7697 (ttp)
REVERT: C  269 MET cc_start: 0.7561 (mtm) cc_final: 0.7017 (mtp)
REVERT: C  311 MET cc_start: 0.8854 (mmt) cc_final: 0.8596 (mmt)
REVERT: C  399 MET cc_start: 0.7667 (ttp) cc_final: 0.7392 (ttp)
  outliers start: 16
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1695
  time to fit residues: 25.2397
Evaluate side-chains
  99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 99 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 318 GLN
B 338 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.138579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.105924 restraints weight = 11171.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.17
r_work: 0.2859 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9618  Z= 0.198
  Angle     :  0.525   7.784  13083  Z= 0.264
  Chirality :  0.037   0.121   1620
  Planarity :  0.004   0.053   1605
  Dihedral  : 10.501  93.666   1488
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.86 %
    Favored  : 84.98 %
  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: 1242
  helix:  1.15 (0.16), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.76 (0.39), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.002   0.000   ARG C 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.927 
Fit side-chains
REVERT: B  310 ASN cc_start: 0.9276 (t0) cc_final: 0.8901 (t0)
REVERT: B  311 MET cc_start: 0.8813 (mmt) cc_final: 0.7977 (mmt)
REVERT: B  395 MET cc_start: 0.8532 (mtm) cc_final: 0.8313 (mtp)
REVERT: B  399 MET cc_start: 0.7641 (ttp) cc_final: 0.7069 (ttp)
REVERT: A  269 MET cc_start: 0.7384 (mtm) cc_final: 0.6889 (mtp)
REVERT: A  399 MET cc_start: 0.7835 (ttp) cc_final: 0.7607 (ttp)
REVERT: C  269 MET cc_start: 0.7335 (mtm) cc_final: 0.6778 (mtp)
REVERT: C  311 MET cc_start: 0.8851 (mmt) cc_final: 0.8475 (mmt)
REVERT: C  399 MET cc_start: 0.7599 (ttp) cc_final: 0.7317 (ttp)
  outliers start: 21
  outliers final: 17
  residues processed: 104
  average time/residue: 0.1634
  time to fit residues: 26.3785
Evaluate side-chains
  106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 114 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 121 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
C 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.137301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.104330 restraints weight = 11278.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.19
r_work: 0.2847 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9618  Z= 0.205
  Angle     :  0.533   7.904  13083  Z= 0.268
  Chirality :  0.038   0.121   1620
  Planarity :  0.005   0.053   1605
  Dihedral  : 10.439  93.067   1488
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.17 %
    Favored  : 84.67 %
  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:  1.33 (0.24), residues: 1242
  helix:  1.22 (0.16), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.49 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.010   0.001   TYR B 254 
 ARG   0.002   0.000   ARG C 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.957 
Fit side-chains
REVERT: B  269 MET cc_start: 0.7241 (mtm) cc_final: 0.6866 (mtp)
REVERT: B  310 ASN cc_start: 0.9303 (t0) cc_final: 0.8879 (t0)
REVERT: B  311 MET cc_start: 0.8848 (mmt) cc_final: 0.7982 (mmt)
REVERT: B  395 MET cc_start: 0.8511 (mtm) cc_final: 0.8288 (mtp)
REVERT: B  399 MET cc_start: 0.7612 (ttp) cc_final: 0.7368 (ttp)
REVERT: A  269 MET cc_start: 0.7367 (mtm) cc_final: 0.6870 (mtp)
REVERT: A  399 MET cc_start: 0.7804 (ttp) cc_final: 0.7565 (ttp)
REVERT: C  269 MET cc_start: 0.7347 (mtm) cc_final: 0.6778 (mtp)
REVERT: C  311 MET cc_start: 0.8851 (mmt) cc_final: 0.8544 (mmt)
REVERT: C  399 MET cc_start: 0.7597 (ttp) cc_final: 0.7299 (ttp)
  outliers start: 21
  outliers final: 18
  residues processed: 99
  average time/residue: 0.1773
  time to fit residues: 27.3988
Evaluate side-chains
  104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0270
   chunk 48 optimal weight:    0.6980
   chunk 114 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.138983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.106406 restraints weight = 11216.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.18
r_work: 0.2882 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9618  Z= 0.168
  Angle     :  0.514   7.952  13083  Z= 0.257
  Chirality :  0.037   0.118   1620
  Planarity :  0.004   0.053   1605
  Dihedral  :  9.999  91.275   1488
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.07 %
    Favored  : 84.98 %
  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:  1.59 (0.24), residues: 1242
  helix:  1.41 (0.17), residues: 1029
  sheet:  None (None), residues: 0
  loop : -0.48 (0.41), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.008   0.001   TYR B 254 
 ARG   0.001   0.000   ARG C 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.975 
Fit side-chains
REVERT: B  202 MET cc_start: 0.7880 (mmm) cc_final: 0.7504 (mmm)
REVERT: B  269 MET cc_start: 0.7224 (mtm) cc_final: 0.6851 (mtp)
REVERT: B  311 MET cc_start: 0.8767 (mmt) cc_final: 0.7932 (mmt)
REVERT: B  395 MET cc_start: 0.8405 (mtm) cc_final: 0.8194 (mtp)
REVERT: B  399 MET cc_start: 0.7593 (ttp) cc_final: 0.7349 (ttp)
REVERT: A  269 MET cc_start: 0.7324 (mtm) cc_final: 0.6865 (mtp)
REVERT: A  399 MET cc_start: 0.7819 (ttp) cc_final: 0.7570 (ttp)
REVERT: C  269 MET cc_start: 0.7356 (mtm) cc_final: 0.6813 (mtp)
REVERT: C  311 MET cc_start: 0.8727 (mmt) cc_final: 0.8519 (mmt)
REVERT: C  399 MET cc_start: 0.7608 (ttp) cc_final: 0.7303 (ttp)
  outliers start: 19
  outliers final: 17
  residues processed: 98
  average time/residue: 0.1640
  time to fit residues: 24.9221
Evaluate side-chains
  102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 115 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 83 optimal weight:    0.3980
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.144100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.111714 restraints weight = 11087.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 2.25
r_work: 0.2877 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9618  Z= 0.175
  Angle     :  0.518   7.828  13083  Z= 0.260
  Chirality :  0.037   0.118   1620
  Planarity :  0.004   0.053   1605
  Dihedral  :  9.948  90.133   1488
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.17 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.24), residues: 1242
  helix:  1.45 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.31 (0.42), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.007   0.001   TYR B 254 
 ARG   0.002   0.000   ARG C 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.932 
Fit side-chains
REVERT: B  202 MET cc_start: 0.7832 (mmm) cc_final: 0.7452 (mmm)
REVERT: B  269 MET cc_start: 0.7052 (mtm) cc_final: 0.6698 (mtp)
REVERT: B  311 MET cc_start: 0.8787 (mmt) cc_final: 0.7919 (mmt)
REVERT: B  395 MET cc_start: 0.8344 (mtm) cc_final: 0.8124 (mtp)
REVERT: B  399 MET cc_start: 0.7537 (ttp) cc_final: 0.7294 (ttp)
REVERT: A  269 MET cc_start: 0.7228 (mtm) cc_final: 0.6747 (mtp)
REVERT: A  399 MET cc_start: 0.7589 (ttp) cc_final: 0.7320 (ttp)
REVERT: C  269 MET cc_start: 0.7240 (mtm) cc_final: 0.6694 (mtp)
REVERT: C  399 MET cc_start: 0.7538 (ttp) cc_final: 0.7227 (ttp)
  outliers start: 18
  outliers final: 16
  residues processed: 98
  average time/residue: 0.1754
  time to fit residues: 26.7488
Evaluate side-chains
  102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 112 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.137854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.105051 restraints weight = 11278.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.19
r_work: 0.2861 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9618  Z= 0.198
  Angle     :  0.535   7.817  13083  Z= 0.267
  Chirality :  0.038   0.120   1620
  Planarity :  0.004   0.053   1605
  Dihedral  : 10.008  89.061   1488
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.68 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1242
  helix:  1.40 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -0.46 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.001   0.000   ARG A 397 

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

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

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2484 Ramachandran restraints generated.
    1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.781 
Fit side-chains
REVERT: B  202 MET cc_start: 0.7901 (mmm) cc_final: 0.7553 (mmm)
REVERT: B  269 MET cc_start: 0.7228 (mtm) cc_final: 0.6849 (mtp)
REVERT: B  311 MET cc_start: 0.8804 (mmt) cc_final: 0.7929 (mmt)
REVERT: B  395 MET cc_start: 0.8410 (mtm) cc_final: 0.8195 (mtp)
REVERT: B  399 MET cc_start: 0.7615 (ttp) cc_final: 0.7374 (ttp)
REVERT: A  269 MET cc_start: 0.7362 (mtm) cc_final: 0.6882 (mtp)
REVERT: A  399 MET cc_start: 0.7853 (ttp) cc_final: 0.7612 (ttp)
REVERT: C  269 MET cc_start: 0.7358 (mtm) cc_final: 0.6794 (mtp)
REVERT: C  399 MET cc_start: 0.7574 (ttp) cc_final: 0.7291 (ttp)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1720
  time to fit residues: 25.3006
Evaluate side-chains
  101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  299 TYR
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  299 TYR
Chi-restraints excluded: chain A residue  392 ILE
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   66 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  169 MET
Chi-restraints excluded: chain C residue  299 TYR
Chi-restraints excluded: chain C residue  392 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0570
   chunk 86 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7498

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.139909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.107168 restraints weight = 11251.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.26
r_work: 0.2855 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9618  Z= 0.196
  Angle     :  0.536   7.783  13083  Z= 0.268
  Chirality :  0.038   0.120   1620
  Planarity :  0.004   0.053   1605
  Dihedral  :  9.973  87.338   1488
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.99 %
    Favored  : 84.47 %
  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:  1.63 (0.24), residues: 1242
  helix:  1.43 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -0.45 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A  40 
 PHE   0.005   0.001   PHE C  50 
 TYR   0.009   0.001   TYR B 254 
 ARG   0.001   0.000   ARG A 397 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3450.30 seconds
wall clock time: 62 minutes 14.15 seconds (3734.15 seconds total)