Starting phenix.real_space_refine
on Thu Aug  6 14:38:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hn1_52304/08_2026/9hn1_52304.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.099
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    5009      2.51       5
     N    1354      2.21       5
     O    1630      1.98       5
     H    7284      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15298
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 4935
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 326}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 4946
          Classifications: {'peptide': 331}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 327}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 5005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 5005
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 332}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 412
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
          Chain breaks: 1
  Time building chain proxies: 2.73, per 1000 atoms: 0.18
  Number of scatterers: 15298
  At special positions: 0
  Unit cell: (73.216, 94.848, 90.688, 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      21     16.00
     O    1630      8.00
     N    1354      7.00
     C    5009      6.00
     H    7284      1.00
    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: 1.34
  Conformation dependent library (CDL) restraints added in 471.8 milliseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1808

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 7 sheets defined
      7.7% alpha, 52.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.939A  pdb=" N   GLU A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A 126 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 220
    Processing helix  chain 'A' and resid 339 through 345
    Processing helix  chain 'B' and resid 106 through 108
      No H-bonds generated for 'chain 'B' and resid 106 through 108'
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 3.807A  pdb=" N   GLU B 124 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ALA B 126 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 186
      removed outlier: 3.958A  pdb=" N   GLN B 186 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 220
    Processing helix  chain 'B' and resid 338 through 345
    Processing helix  chain 'C' and resid 120 through 126
      removed outlier: 3.896A  pdb=" N   GLU C 124 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ALA C 126 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 146
    Processing helix  chain 'C' and resid 182 through 186
      removed outlier: 3.757A  pdb=" N   GLN C 186 " --> pdb=" O   ILE C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 215 through 220
      removed outlier: 3.621A  pdb=" N   ALA C 220 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 345
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34
      removed outlier: 3.802A  pdb=" N   LEU A  98 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ASN A  82 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   THR A  96 " --> pdb=" O   ASN A  82 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   ASP A  84 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR A  94 " --> pdb=" O   ASP A  84 " (cutoff:3.500A)
      removed outlier: 12.286A  pdb=" N   ARG A  97 " --> pdb=" O   TYR A 117 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   TYR A 117 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   ASN A 116 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   ASN A 150 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   ARG A 282 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   THR A 316 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   SER A 284 " --> pdb=" O   VAL A 314 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   VAL A 314 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   GLY A 286 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL A 312 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   VAL A 288 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LYS A 310 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   THR A 290 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASP A 294 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   GLY A 304 " --> pdb=" O   ASP A 294 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL A 314 " --> pdb=" O   TYR A 330 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ALA A 328 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 28
      removed outlier: 4.081A  pdb=" N   TYR B  26 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ASN B 116 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ASN B 150 " --> pdb=" O   ASN B 116 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   VAL B 309 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLY B 292 " --> pdb=" O   ASP B 307 " (cutoff:3.500A)
      removed outlier: 5.190A  pdb=" N   ASP B 307 " --> pdb=" O   GLY B 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 38
    Processing sheet with id=AA5, first strand: chain 'C' and resid 24 through 27
      removed outlier: 3.822A  pdb=" N   TYR C  26 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 27
      removed outlier: 3.822A  pdb=" N   TYR C  26 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   THR C  74 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   LEU C 103 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR C  76 " --> pdb=" O   ALA C 101 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   ALA C 101 " --> pdb=" O   TYR C  76 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   GLN C  78 " --> pdb=" O   ALA C  99 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ALA C  99 " --> pdb=" O   GLN C  78 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   GLU C  80 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
      removed outlier: 12.388A  pdb=" N   ARG C  97 " --> pdb=" O   TYR C 117 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   TYR C 117 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ASN C 116 " --> pdb=" O   ASN C 150 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   ASN C 150 " --> pdb=" O   ASN C 116 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLY C 292 " --> pdb=" O   ASP C 307 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   ASP C 307 " --> pdb=" O   GLY C 292 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASP C 294 " --> pdb=" O   ASP C 305 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ASP C 305 " --> pdb=" O   ASP C 294 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLN C 351 " --> pdb=" O   LYS C 331 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR C 358 " --> pdb=" O   MET C  39 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   MET C  39 " --> pdb=" O   TYR C 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 250 through 251

    451 hydrogen bonds defined for protein.
    1248 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: 3.60

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7284
        1.03 -     1.23: 1
        1.23 -     1.42: 3840
        1.42 -     1.62: 4313
        1.62 -     1.81: 42
  Bond restraints: 15480
  Sorted by residual:
  bond pdb=" CA  GLY A 147 "
       pdb=" C   GLY A 147 "
    ideal  model  delta    sigma   weight residual
    1.516  1.506  0.010 1.03e-02 9.43e+03 1.03e+00
  bond pdb=" SD  MET B  83 "
       pdb=" CE  MET B  83 "
    ideal  model  delta    sigma   weight residual
    1.791  1.770  0.021 2.50e-02 1.60e+03 7.29e-01
  bond pdb=" C   THR B  74 "
       pdb=" N   GLY B  75 "
    ideal  model  delta    sigma   weight residual
    1.331  1.322  0.009 1.10e-02 8.26e+03 6.84e-01
  bond pdb=" CB  TRP C  79 "
       pdb=" CG  TRP C  79 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.62e-01
  bond pdb=" CA  GLY A  62 "
       pdb=" C   GLY A  62 "
    ideal  model  delta    sigma   weight residual
    1.519  1.511  0.008 1.01e-02 9.80e+03 6.37e-01
  ... (remaining 15475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.94: 25669
        0.94 -     1.87: 1682
        1.87 -     2.81: 98
        2.81 -     3.75: 24
        3.75 -     4.69: 6
  Bond angle restraints: 27479
  Sorted by residual:
  angle pdb=" C   TYR A 144 "
        pdb=" CA  TYR A 144 "
        pdb=" CB  TYR A 144 "
      ideal   model   delta    sigma   weight residual
     116.54  111.87    4.67 1.15e+00 7.56e-01 1.65e+01
  angle pdb=" C   TYR C 144 "
        pdb=" CA  TYR C 144 "
        pdb=" CB  TYR C 144 "
      ideal   model   delta    sigma   weight residual
     115.79  111.30    4.49 1.19e+00 7.06e-01 1.42e+01
  angle pdb=" N   GLY C 114 "
        pdb=" CA  GLY C 114 "
        pdb=" C   GLY C 114 "
      ideal   model   delta    sigma   weight residual
     110.29  113.53   -3.24 1.28e+00 6.10e-01 6.40e+00
  angle pdb=" CA  GLY B 134 "
        pdb=" C   GLY B 134 "
        pdb=" O   GLY B 134 "
      ideal   model   delta    sigma   weight residual
     122.24  120.11    2.13 8.70e-01 1.32e+00 6.01e+00
  angle pdb=" CA  GLY B 134 "
        pdb=" C   GLY B 134 "
        pdb=" N   GLY B 135 "
      ideal   model   delta    sigma   weight residual
     115.13  117.40   -2.27 1.05e+00 9.07e-01 4.69e+00
  ... (remaining 27474 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6565
       17.98 -    35.96: 610
       35.96 -    53.94: 193
       53.94 -    71.93: 40
       71.93 -    89.91: 12
  Dihedral angle restraints: 7420
    sinusoidal: 3778
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CG  ARG C 342 "
           pdb=" CD  ARG C 342 "
           pdb=" NE  ARG C 342 "
           pdb=" CZ  ARG C 342 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -38.90  -51.10     2      1.50e+01 4.44e-03 1.29e+01
  dihedral pdb=" CB  GLU A  80 "
           pdb=" CG  GLU A  80 "
           pdb=" CD  GLU A  80 "
           pdb=" OE1 GLU A  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.91   89.91     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU C  80 "
           pdb=" CG  GLU C  80 "
           pdb=" CD  GLU C  80 "
           pdb=" OE1 GLU C  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.70  -89.70     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 546
       0.027 -    0.053: 418
       0.053 -    0.079: 74
       0.079 -    0.106: 34
       0.106 -    0.132: 30
  Chirality restraints: 1102
  Sorted by residual:
  chirality pdb=" CA  VAL A 326 "
            pdb=" N   VAL A 326 "
            pdb=" C   VAL A 326 "
            pdb=" CB  VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  ILE A 285 "
            pdb=" N   ILE A 285 "
            pdb=" C   ILE A 285 "
            pdb=" CB  ILE A 285 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  VAL A 312 "
            pdb=" N   VAL A 312 "
            pdb=" C   VAL A 312 "
            pdb=" CB  VAL A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 1099 not shown)

  Planarity restraints: 2487
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 342 "    0.223 9.50e-02 1.11e+02   7.47e-02 6.49e+00
        pdb=" NE  ARG C 342 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 342 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 342 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 342 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG C 342 "   -0.007 2.00e-02 2.50e+03
        pdb="HH12 ARG C 342 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG C 342 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG C 342 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 282 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO A 283 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 282 "   -0.023 5.00e-02 4.00e+02   3.43e-02 1.89e+00
        pdb=" N   PRO B 283 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 283 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 283 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2484 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1055
        2.19 -     2.80: 30516
        2.80 -     3.40: 39981
        3.40 -     4.00: 56829
        4.00 -     4.60: 87269
  Nonbonded interactions: 215650
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 323 "
            pdb=" H   GLN B 359 "
     model   vdw
     1.592 2.450
  nonbonded pdb="HD22 ASN A 321 "
            pdb=" OG1 THR B  67 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASN C 321 "
            pdb=" H   LYS C 322 "
     model   vdw
     1.627 2.450
  nonbonded pdb=" HE2 HIS B 184 "
            pdb=" O   GLY B 259 "
     model   vdw
     1.633 2.450
  nonbonded pdb=" OE2 GLU A  80 "
            pdb=" HE  ARG A  97 "
     model   vdw
     1.635 2.450
  ... (remaining 215645 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 23 through 42 or (resid 43 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 
2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ 
E1)) or resid 44 through 46 or (resid 47 and (name N or name CA or name C or nam \ 
e O or name CB or name H or name HA )) or resid 51 through 159 or (resid 160 and \ 
 (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ 
sid 164 through 302 or resid 305 through 360))
  selection = (chain 'B' and (resid 23 through 46 or (resid 47 and (name N or name CA or name  \ 
C or name O or name CB or name H or name HA )) or resid 51 through 295 or (resid \ 
 296 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 
 or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG2 or name  \ 
HG3 or name HE21 or name HE22)) or resid 297 through 335 or resid 338 through 36 \ 
0))
  selection = (chain 'C' and (resid 23 through 47 or resid 51 through 159 or (resid 160 and (n \ 
ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 
 164 through 295 or (resid 296 and (name N or name CA or name C or name O or nam \ 
e CB or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or nam \ 
e HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 297 through 3 \ 
02 or resid 305 through 335 or resid 338 through 360))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.540
  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:             0.080
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.190
  Find NCS groups from input model:        0.260
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
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      :  0.003   0.025   8196  Z= 0.156
  Angle     :  0.502   4.687  11093  Z= 0.301
  Chirality :  0.040   0.132   1102
  Planarity :  0.004   0.097   1485
  Dihedral  : 15.739  89.907   2833
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.38 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.27), residues: 1000
  helix: -1.45 (0.69), residues: 51
  sheet: -0.23 (0.22), residues: 549
  loop : -1.45 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 342 
 TYR   0.012   0.001   TYR C 358 
 PHE   0.008   0.001   PHE B 100 
 TRP   0.013   0.001   TRP B 317 
 HIS   0.002   0.001   HIS C 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.16 ( 8196)
  covalent geometry    : angle       0.50241 /  0.30 (11093)
  hydrogen bonds       : bond        0.09968 /  7.12 (  426)
  hydrogen bonds       : angle       6.30672 /  4.21 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  134 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7318 (tttm)
REVERT: A  117 TYR cc_start: 0.9110 (m-80) cc_final: 0.8898 (m-80)
REVERT: A  228 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8137 (mt-10)
REVERT: B   32 LYS cc_start: 0.7910 (tttt) cc_final: 0.7628 (ttmt)
REVERT: B   68 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7808 (tp40)
REVERT: B  219 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8440 (mttt)
REVERT: B  307 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8363 (p0)
REVERT: B  334 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.6810 (mp10)
REVERT: C   34 ASP cc_start: 0.8547 (t0) cc_final: 0.8202 (t70)
REVERT: C  124 GLU cc_start: 0.8935 (tp30) cc_final: 0.8612 (tp30)
REVERT: C  160 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6815 (m-80)
REVERT: C  236 TYR cc_start: 0.8810 (t80) cc_final: 0.8485 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 132
  average time/residue: 0.1701
  time to fit residues: 31.6747
Evaluate side-chains
  131 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  182 SER
Chi-restraints excluded: chain B residue  221 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  149 THR
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  223 ASN
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  350 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  27 ASN
A  31 ASN
A 239 ASN
** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 ASN
C 143 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.099995 restraints weight = 29495.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.99
r_work: 0.2954 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (11 function evaluations)
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.0794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   8196  Z= 0.218
  Angle     :  0.494   3.975  11093  Z= 0.282
  Chirality :  0.041   0.131   1102
  Planarity :  0.004   0.058   1485
  Dihedral  :  5.949  59.881   1162
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.38 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.27), residues: 1000
  helix: -1.13 (0.74), residues: 51
  sheet: -0.30 (0.22), residues: 542
  loop : -1.51 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 342 
 TYR   0.016   0.001   TYR C 358 
 PHE   0.010   0.001   PHE B 100 
 TRP   0.013   0.001   TRP B 317 
 HIS   0.005   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.22 ( 8196)
  covalent geometry    : angle       0.49395 /  0.28 (11093)
  hydrogen bonds       : bond        0.03195 /  2.17 (  426)
  hydrogen bonds       : angle       5.51501 /  3.78 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  143 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7635 (tttm)
REVERT: A  301 PHE cc_start: 0.8058 (t80) cc_final: 0.7768 (t80)
REVERT: B   68 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7867 (tp40)
REVERT: B  103 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9119 (mt)
REVERT: B  219 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8471 (mttt)
REVERT: B  312 VAL cc_start: 0.9220 (p) cc_final: 0.8989 (p)
REVERT: B  334 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7166 (mp10)
REVERT: C   34 ASP cc_start: 0.8618 (t0) cc_final: 0.8316 (t70)
REVERT: C   84 ASP cc_start: 0.8844 (t0) cc_final: 0.8613 (t0)
REVERT: C  160 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.6771 (m-80)
REVERT: C  236 TYR cc_start: 0.8932 (t80) cc_final: 0.8652 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1521
  time to fit residues: 29.4297
Evaluate side-chains
  125 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  316 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  31 ASN
A 150 ASN
C 177 ASN
C 187 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.116220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.098224 restraints weight = 29774.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 1.98
r_work: 0.2924 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   8196  Z= 0.222
  Angle     :  0.491   3.998  11093  Z= 0.281
  Chirality :  0.041   0.128   1102
  Planarity :  0.003   0.051   1485
  Dihedral  :  5.532  59.786   1145
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.37 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.27), residues: 1000
  helix: -1.08 (0.72), residues: 51
  sheet: -0.34 (0.22), residues: 546
  loop : -1.55 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 342 
 TYR   0.016   0.001   TYR C 358 
 PHE   0.010   0.001   PHE B 100 
 TRP   0.013   0.001   TRP B 317 
 HIS   0.004   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.22 ( 8196)
  covalent geometry    : angle       0.49060 /  0.28 (11093)
  hydrogen bonds       : bond        0.03091 /  2.11 (  426)
  hydrogen bonds       : angle       5.42898 /  3.73 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  135 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7596 (tttm)
REVERT: A  301 PHE cc_start: 0.8135 (t80) cc_final: 0.7892 (t80)
REVERT: B   66 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7962 (mt-10)
REVERT: B   68 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7955 (tp40)
REVERT: B  103 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9125 (mt)
REVERT: B  219 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8372 (mttt)
REVERT: B  307 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7951 (p0)
REVERT: B  312 VAL cc_start: 0.9224 (p) cc_final: 0.9009 (p)
REVERT: B  334 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7152 (mp10)
REVERT: C  236 TYR cc_start: 0.8961 (t80) cc_final: 0.8688 (t80)
  outliers start: 25
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1561
  time to fit residues: 28.5608
Evaluate side-chains
  125 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  187 ASN
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  31 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 = 0.3278 r_free = 0.3278 target = 0.116519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.098347 restraints weight = 29735.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.02
r_work: 0.2919 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8765
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8196  Z= 0.197
  Angle     :  0.475   4.043  11093  Z= 0.273
  Chirality :  0.041   0.130   1102
  Planarity :  0.003   0.051   1485
  Dihedral  :  5.475  59.620   1145
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.75 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.27), residues: 1000
  helix: -0.86 (0.72), residues: 51
  sheet: -0.37 (0.22), residues: 546
  loop : -1.54 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 342 
 TYR   0.016   0.001   TYR C 358 
 PHE   0.010   0.001   PHE B 100 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.20 ( 8196)
  covalent geometry    : angle       0.47470 /  0.27 (11093)
  hydrogen bonds       : bond        0.02904 /  1.99 (  426)
  hydrogen bonds       : angle       5.36478 /  3.69 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7547 (tttm)
REVERT: A  301 PHE cc_start: 0.8161 (t80) cc_final: 0.7958 (t80)
REVERT: B   68 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7903 (mm-40)
REVERT: B  103 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9111 (mt)
REVERT: B  219 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8317 (mttt)
REVERT: B  289 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7759 (tt0)
REVERT: B  307 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7949 (p0)
REVERT: B  334 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7213 (mp10)
REVERT: C  236 TYR cc_start: 0.8961 (t80) cc_final: 0.8700 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1586
  time to fit residues: 28.7819
Evaluate side-chains
  128 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.8588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 187 ASN
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.114996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.096886 restraints weight = 29825.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.98
r_work: 0.2898 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2765 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2774
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2774 r_free = 0.2774    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2774
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   8196  Z= 0.238
  Angle     :  0.493   4.093  11093  Z= 0.283
  Chirality :  0.041   0.130   1102
  Planarity :  0.003   0.046   1485
  Dihedral  :  5.558  59.885   1145
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.20 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.12 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.27), residues: 1000
  helix: -0.91 (0.68), residues: 52
  sheet: -0.41 (0.23), residues: 546
  loop : -1.59 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 342 
 TYR   0.017   0.001   TYR C 358 
 PHE   0.011   0.001   PHE B 100 
 TRP   0.015   0.001   TRP B 317 
 HIS   0.004   0.001   HIS B 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.24 ( 8196)
  covalent geometry    : angle       0.49257 /  0.28 (11093)
  hydrogen bonds       : bond        0.02980 /  2.04 (  426)
  hydrogen bonds       : angle       5.39595 /  3.71 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 103
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7692 (tttm)
REVERT: B  103 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9109 (mt)
REVERT: B  219 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8293 (mttt)
REVERT: B  289 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7752 (tt0)
REVERT: B  307 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7966 (p0)
REVERT: B  334 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7212 (mp10)
REVERT: C  236 TYR cc_start: 0.8986 (t80) cc_final: 0.8714 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 127
  average time/residue: 0.1668
  time to fit residues: 30.0557
Evaluate side-chains
  125 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  187 ASN
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 75 optimal weight:    0.1980
   chunk 63 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.117126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.099157 restraints weight = 29370.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.96
r_work: 0.2932 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2813
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2813 r_free = 0.2813    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2813
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8196  Z= 0.142
  Angle     :  0.451   4.118  11093  Z= 0.259
  Chirality :  0.041   0.130   1102
  Planarity :  0.003   0.042   1485
  Dihedral  :  5.429  59.050   1145
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.38 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.27), residues: 1000
  helix: -0.89 (0.66), residues: 58
  sheet: -0.37 (0.23), residues: 546
  loop : -1.54 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 115 
 TYR   0.015   0.001   TYR C 358 
 PHE   0.008   0.001   PHE B 100 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.002   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.14 ( 8196)
  covalent geometry    : angle       0.45067 /  0.26 (11093)
  hydrogen bonds       : bond        0.02709 /  1.85 (  426)
  hydrogen bonds       : angle       5.27305 /  3.62 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  127 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7571 (tttm)
REVERT: B  103 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9094 (mt)
REVERT: B  219 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8293 (mttt)
REVERT: B  289 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7696 (tt0)
REVERT: B  307 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7947 (p0)
REVERT: B  334 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7273 (mp10)
REVERT: C  132 GLU cc_start: 0.8238 (tp30) cc_final: 0.7941 (tp30)
REVERT: C  228 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7395 (mt-10)
REVERT: C  236 TYR cc_start: 0.8967 (t80) cc_final: 0.8723 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1733
  time to fit residues: 30.5485
Evaluate side-chains
  121 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 323 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 = 0.3287 r_free = 0.3287 target = 0.117017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099060 restraints weight = 29334.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.97
r_work: 0.2928 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2807
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2807 r_free = 0.2807    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2807
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   8196  Z= 0.149
  Angle     :  0.445   4.092  11093  Z= 0.256
  Chirality :  0.040   0.130   1102
  Planarity :  0.003   0.043   1485
  Dihedral  :  5.305  58.822   1144
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.01 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.27), residues: 1000
  helix: -0.71 (0.66), residues: 58
  sheet: -0.37 (0.23), residues: 547
  loop : -1.56 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 342 
 TYR   0.015   0.001   TYR C 358 
 PHE   0.009   0.001   PHE B 100 
 TRP   0.014   0.001   TRP B 317 
 HIS   0.003   0.001   HIS B 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 8196)
  covalent geometry    : angle       0.44535 /  0.26 (11093)
  hydrogen bonds       : bond        0.02644 /  1.81 (  426)
  hydrogen bonds       : angle       5.18655 /  3.56 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7603 (tttm)
REVERT: A  117 TYR cc_start: 0.9246 (m-80) cc_final: 0.8952 (m-80)
REVERT: B  144 TYR cc_start: 0.8882 (m-80) cc_final: 0.8634 (m-80)
REVERT: B  219 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8292 (mttt)
REVERT: B  289 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7762 (tt0)
REVERT: B  307 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7955 (p0)
REVERT: B  334 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7335 (mp10)
REVERT: C  132 GLU cc_start: 0.8209 (tp30) cc_final: 0.7911 (tp30)
REVERT: C  228 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7352 (mt-10)
REVERT: C  236 TYR cc_start: 0.8967 (t80) cc_final: 0.8747 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1805
  time to fit residues: 31.0382
Evaluate side-chains
  119 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 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 = 0.3281 r_free = 0.3281 target = 0.116617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.098818 restraints weight = 29789.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 1.95
r_work: 0.2931 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (10 function evaluations)
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8196  Z= 0.161
  Angle     :  0.448   4.078  11093  Z= 0.257
  Chirality :  0.040   0.130   1102
  Planarity :  0.003   0.045   1485
  Dihedral  :  5.297  58.671   1144
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.50 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.27), residues: 1000
  helix: -0.75 (0.66), residues: 58
  sheet: -0.39 (0.23), residues: 547
  loop : -1.56 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 342 
 TYR   0.015   0.001   TYR A 108 
 PHE   0.009   0.001   PHE B 100 
 TRP   0.013   0.001   TRP B 317 
 HIS   0.002   0.001   HIS B 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.16 ( 8196)
  covalent geometry    : angle       0.44780 /  0.26 (11093)
  hydrogen bonds       : bond        0.02661 /  1.82 (  426)
  hydrogen bonds       : angle       5.16389 /  3.55 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7602 (tttm)
REVERT: A  117 TYR cc_start: 0.9247 (m-80) cc_final: 0.8962 (m-80)
REVERT: B  219 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8285 (mttt)
REVERT: B  289 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7719 (tt0)
REVERT: B  307 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7952 (p0)
REVERT: B  334 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7377 (mp10)
REVERT: C  132 GLU cc_start: 0.8211 (tp30) cc_final: 0.7914 (tp30)
REVERT: C  228 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7342 (mt-10)
REVERT: C  236 TYR cc_start: 0.8972 (t80) cc_final: 0.8760 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1806
  time to fit residues: 31.1197
Evaluate side-chains
  118 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 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 = 0.3284 r_free = 0.3284 target = 0.116802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099066 restraints weight = 29339.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 1.94
r_work: 0.2931 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2769 r_free = 0.2769    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8196  Z= 0.157
  Angle     :  0.447   4.101  11093  Z= 0.257
  Chirality :  0.040   0.129   1102
  Planarity :  0.003   0.042   1485
  Dihedral  :  5.272  58.237   1144
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 20.88 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.27), residues: 1000
  helix: -0.77 (0.62), residues: 64
  sheet: -0.42 (0.23), residues: 542
  loop : -1.52 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 342 
 TYR   0.015   0.001   TYR C 358 
 PHE   0.009   0.001   PHE B 100 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.003   0.001   HIS B 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 ( 8196)
  covalent geometry    : angle       0.44692 /  0.26 (11093)
  hydrogen bonds       : bond        0.02641 /  1.80 (  426)
  hydrogen bonds       : angle       5.14411 /  3.53 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7573 (tttm)
REVERT: A  117 TYR cc_start: 0.9241 (m-80) cc_final: 0.8950 (m-80)
REVERT: B  219 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8285 (mttt)
REVERT: B  289 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7701 (tt0)
REVERT: B  307 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7959 (p0)
REVERT: B  334 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7335 (mp10)
REVERT: C  132 GLU cc_start: 0.8202 (tp30) cc_final: 0.7906 (tp30)
REVERT: C  228 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7308 (mt-10)
REVERT: C  236 TYR cc_start: 0.8971 (t80) cc_final: 0.8770 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 117
  average time/residue: 0.1780
  time to fit residues: 29.9246
Evaluate side-chains
  117 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 323 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 = 0.3261 r_free = 0.3261 target = 0.115262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.097326 restraints weight = 29747.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.96
r_work: 0.2908 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8770
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8196  Z= 0.206
  Angle     :  0.470   4.100  11093  Z= 0.270
  Chirality :  0.041   0.128   1102
  Planarity :  0.003   0.042   1485
  Dihedral  :  5.371  58.471   1144
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.13 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.27), residues: 1000
  helix: -0.72 (0.67), residues: 58
  sheet: -0.46 (0.23), residues: 549
  loop : -1.57 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 342 
 TYR   0.016   0.001   TYR C 358 
 PHE   0.010   0.001   PHE B 100 
 TRP   0.012   0.001   TRP B 317 
 HIS   0.003   0.001   HIS B 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.21 ( 8196)
  covalent geometry    : angle       0.46981 /  0.27 (11093)
  hydrogen bonds       : bond        0.02793 /  1.92 (  426)
  hydrogen bonds       : angle       5.23146 /  3.59 ( 1248)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR   47 is missing expected H atoms. Skipping.
Residue LYS   50 is missing expected H atoms. Skipping.
Evaluate side-chains
  116 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7629 (tttm)
REVERT: B  219 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8288 (mttt)
REVERT: B  289 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7735 (tt0)
REVERT: B  307 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8003 (p0)
REVERT: B  334 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7368 (mp10)
REVERT: C  132 GLU cc_start: 0.8235 (tp30) cc_final: 0.7952 (tp30)
REVERT: C  228 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7349 (mt-10)
REVERT: C  236 TYR cc_start: 0.9017 (t80) cc_final: 0.8811 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1777
  time to fit residues: 28.7056
Evaluate side-chains
  116 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  150 ASN
Chi-restraints excluded: chain B residue  179 HIS
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  187 ASN
Chi-restraints excluded: chain B residue  279 PHE
Chi-restraints excluded: chain B residue  289 GLN
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  334 GLN
Chi-restraints excluded: chain C residue  110 SER
Chi-restraints excluded: chain C residue  160 PHE
Chi-restraints excluded: chain C residue  169 PHE
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  266 THR
Chi-restraints excluded: chain C residue  349 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0020
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 81 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.8790

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.098957 restraints weight = 29294.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.99
r_work: 0.2930 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2805
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2805 r_free = 0.2805    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2805
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8196  Z= 0.133
  Angle     :  0.441   4.155  11093  Z= 0.253
  Chirality :  0.040   0.130   1102
  Planarity :  0.003   0.041   1485
  Dihedral  :  5.250  57.395   1144
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 21.13 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.27), residues: 1000
  helix: -0.57 (0.69), residues: 58
  sheet: -0.40 (0.23), residues: 542
  loop : -1.47 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 342 
 TYR   0.014   0.001   TYR C 358 
 PHE   0.008   0.001   PHE B 100 
 TRP   0.013   0.001   TRP B 317 
 HIS   0.002   0.001   HIS A 184 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.13 ( 8196)
  covalent geometry    : angle       0.44141 /  0.25 (11093)
  hydrogen bonds       : bond        0.02563 /  1.76 (  426)
  hydrogen bonds       : angle       5.10585 /  3.50 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3526.39 seconds
wall clock time: 60 minutes 44.45 seconds (3644.45 seconds total)