Starting phenix.real_space_refine
on Tue Feb  3 23:57:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kd6_62263/02_2026/9kd6_62263.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4970      2.51       5
     N    1258      2.21       5
     O    1480      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7740
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 3870
          Classifications: {'peptide': 507}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 461}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 3870
          Classifications: {'peptide': 507}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 45, 'TRANS': 461}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.58, per 1000 atoms: 0.20
  Number of scatterers: 7740
  At special positions: 0
  Unit cell: (102, 80.24, 103.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1480      8.00
     N    1258      7.00
     C    4970      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 242.2 milliseconds
  

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1852

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 15 sheets defined
      7.7% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 83
    Processing helix  chain 'A' and resid 84 through 86
      No H-bonds generated for 'chain 'A' and resid 84 through 86'
    Processing helix  chain 'A' and resid 217 through 221
    Processing helix  chain 'A' and resid 263 through 268
      removed outlier: 3.651A  pdb=" N   TRP A 268 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 396
      removed outlier: 3.692A  pdb=" N   ILE A 396 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 455
      removed outlier: 3.774A  pdb=" N   ILE A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER A 454 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ALA A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 83
    Processing helix  chain 'B' and resid 84 through 86
      No H-bonds generated for 'chain 'B' and resid 84 through 86'
    Processing helix  chain 'B' and resid 123 through 128
    Processing helix  chain 'B' and resid 136 through 140
      removed outlier: 3.716A  pdb=" N   THR B 139 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ALA B 140 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 136 through 140'
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 390 through 396
      removed outlier: 3.729A  pdb=" N   ILE B 396 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 454
      removed outlier: 3.756A  pdb=" N   ILE B 452 " --> pdb=" O   SER B 448 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   SER B 454 " --> pdb=" O   ASP B 450 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36
      removed outlier: 3.616A  pdb=" N   PHE A 196 " --> pdb=" O   ASN A  36 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A  88 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 56
      removed outlier: 12.489A  pdb=" N   GLU A  48 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 10.100A  pdb=" N   SER A 188 " --> pdb=" O   PRO A  50 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   GLY A  52 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 143 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 136
      removed outlier: 3.707A  pdb=" N   LEU A 135 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LYS A 108 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 444
      removed outlier: 7.642A  pdb=" N   ARG A 422 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 251
    Processing sheet with id=AA6, first strand: chain 'B' and resid 428 through 429
      removed outlier: 6.207A  pdb=" N   TYR A 338 " --> pdb=" O   SER B 429 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   MET A 345 " --> pdb=" O   SER A 367 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   TRP A 285 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   GLY A 277 " --> pdb=" O   TRP A 285 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ILE A 287 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 9.471A  pdb=" N   VAL A 325 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ILE A 381 " --> pdb=" O   VAL A 325 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 327 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A 324 " --> pdb=" O   MET A 345 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   MET A 345 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   CYS A 326 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA A 343 " --> pdb=" O   CYS A 326 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   THR A 328 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 341 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 429
      removed outlier: 5.760A  pdb=" N   ALA A 427 " --> pdb=" O   TYR B 338 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   ASP B 340 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   SER A 429 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   ASP B 342 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET B 345 " --> pdb=" O   SER B 367 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   TRP B 285 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   GLY B 277 " --> pdb=" O   TRP B 285 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE B 287 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLU B 275 " --> pdb=" O   ILE B 287 " (cutoff:3.500A)
      removed outlier: 13.726A  pdb=" N   PHE B 327 " --> pdb=" O   ARG B 377 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE B 379 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
      removed outlier: 8.375A  pdb=" N   ILE B 381 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 15.146A  pdb=" N   GLU B 331 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 6.171A  pdb=" N   CYS B 326 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B 343 " --> pdb=" O   CYS B 326 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   THR B 328 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   VAL B 341 " --> pdb=" O   THR B 328 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 489 through 490
      removed outlier: 3.962A  pdb=" N   VAL A 477 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ALA A 465 " --> pdb=" O   TRP A 513 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   TRP A 513 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A 467 " --> pdb=" O   ASN A 511 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A 507 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 36
      removed outlier: 4.031A  pdb=" N   PHE B 196 " --> pdb=" O   ASN B  36 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS B 195 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 56
      removed outlier: 6.206A  pdb=" N   LEU B 186 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   GLY B  51 " --> pdb=" O   ILE B 184 " (cutoff:3.500A)
      removed outlier: 10.913A  pdb=" N   ILE B 184 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 10.310A  pdb=" N   THR B  53 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 11.614A  pdb=" N   ILE B 182 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 133
      removed outlier: 6.485A  pdb=" N   LYS B 108 " --> pdb=" O   TYR B 170 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 234 through 236
    Processing sheet with id=AB4, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AB5, first strand: chain 'B' and resid 423 through 425
    Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490
      removed outlier: 3.916A  pdb=" N   VAL B 477 " --> pdb=" O   LEU B 472 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ALA B 465 " --> pdb=" O   TRP B 513 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   TRP B 513 " --> pdb=" O   ALA B 465 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU B 467 " --> pdb=" O   ASN B 511 " (cutoff:3.500A)

    144 hydrogen bonds defined for protein.
    369 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: 0.82

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2481
        1.34 -     1.46: 1746
        1.46 -     1.58: 3691
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 7974
  Sorted by residual:
  bond pdb=" N   GLY A 159 "
       pdb=" CA  GLY A 159 "
    ideal  model  delta    sigma   weight residual
    1.445  1.477 -0.032 8.30e-03 1.45e+04 1.53e+01
  bond pdb=" N   PHE B 130 "
       pdb=" CA  PHE B 130 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.034 9.20e-03 1.18e+04 1.39e+01
  bond pdb=" N   PRO B 300 "
       pdb=" CD  PRO B 300 "
    ideal  model  delta    sigma   weight residual
    1.473  1.517 -0.044 1.40e-02 5.10e+03 9.83e+00
  bond pdb=" N   TYR B 155 "
       pdb=" CA  TYR B 155 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.18e-02 7.18e+03 8.41e+00
  bond pdb=" N   ILE A 287 "
       pdb=" CA  ILE A 287 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.20e-02 6.94e+03 8.34e+00
  ... (remaining 7969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 10376
        1.54 -     3.08: 472
        3.08 -     4.62: 76
        4.62 -     6.16: 10
        6.16 -     7.69: 4
  Bond angle restraints: 10938
  Sorted by residual:
  angle pdb=" N   GLY A 163 "
        pdb=" CA  GLY A 163 "
        pdb=" C   GLY A 163 "
      ideal   model   delta    sigma   weight residual
     114.10  107.13    6.97 1.51e+00 4.39e-01 2.13e+01
  angle pdb=" N   ASN A 152 "
        pdb=" CA  ASN A 152 "
        pdb=" C   ASN A 152 "
      ideal   model   delta    sigma   weight residual
     114.12  108.20    5.92 1.39e+00 5.18e-01 1.81e+01
  angle pdb=" N   ASN B 152 "
        pdb=" CA  ASN B 152 "
        pdb=" C   ASN B 152 "
      ideal   model   delta    sigma   weight residual
     113.28  108.40    4.88 1.22e+00 6.72e-01 1.60e+01
  angle pdb=" CA  GLY A 159 "
        pdb=" C   GLY A 159 "
        pdb=" O   GLY A 159 "
      ideal   model   delta    sigma   weight residual
     121.72  118.12    3.60 9.60e-01 1.09e+00 1.41e+01
  angle pdb=" CA  GLY A  88 "
        pdb=" C   GLY A  88 "
        pdb=" O   GLY A  88 "
      ideal   model   delta    sigma   weight residual
     121.47  118.13    3.34 9.00e-01 1.23e+00 1.38e+01
  ... (remaining 10933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 4374
       16.44 -    32.88: 242
       32.88 -    49.32: 42
       49.32 -    65.75: 8
       65.75 -    82.19: 6
  Dihedral angle restraints: 4672
    sinusoidal: 1766
      harmonic: 2906
  Sorted by residual:
  dihedral pdb=" CD  ARG A 286 "
           pdb=" NE  ARG A 286 "
           pdb=" CZ  ARG A 286 "
           pdb=" NH1 ARG A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.19   82.19     1      1.00e+01 1.00e-02 8.30e+01
  dihedral pdb=" CD  ARG A 158 "
           pdb=" NE  ARG A 158 "
           pdb=" CZ  ARG A 158 "
           pdb=" NH1 ARG A 158 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.57  -80.57     1      1.00e+01 1.00e-02 8.03e+01
  dihedral pdb=" CD  ARG B 321 "
           pdb=" NE  ARG B 321 "
           pdb=" CZ  ARG B 321 "
           pdb=" NH1 ARG B 321 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -71.71   71.71     1      1.00e+01 1.00e-02 6.59e+01
  ... (remaining 4669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 844
       0.043 -    0.086: 231
       0.086 -    0.130: 123
       0.130 -    0.173: 17
       0.173 -    0.216: 5
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" CA  ARG B 158 "
            pdb=" N   ARG B 158 "
            pdb=" C   ARG B 158 "
            pdb=" CB  ARG B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE A 150 "
            pdb=" N   ILE A 150 "
            pdb=" C   ILE A 150 "
            pdb=" CB  ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE B 150 "
            pdb=" N   ILE B 150 "
            pdb=" C   ILE B 150 "
            pdb=" CB  ILE B 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1217 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 286 "   -1.088 9.50e-02 1.11e+02   4.87e-01 1.43e+02
        pdb=" NE  ARG A 286 "    0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 286 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 286 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 286 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 158 "   -1.085 9.50e-02 1.11e+02   4.86e-01 1.43e+02
        pdb=" NE  ARG A 158 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 158 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 158 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 158 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 321 "   -1.037 9.50e-02 1.11e+02   4.65e-01 1.31e+02
        pdb=" NE  ARG B 321 "    0.062 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 321 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 321 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 321 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 57
        2.52 -     3.12: 5840
        3.12 -     3.71: 11154
        3.71 -     4.31: 15305
        4.31 -     4.90: 26538
  Nonbonded interactions: 58894
  Sorted by model distance:
  nonbonded pdb=" CB  SER A  27 "
            pdb=" NZ  LYS A 151 "
     model   vdw
     1.928 3.520
  nonbonded pdb=" O   TYR B  86 "
            pdb=" NH2 ARG B 158 "
     model   vdw
     2.082 3.120
  nonbonded pdb=" CB  ALA A 274 "
            pdb=" CD2 LEU A 372 "
     model   vdw
     2.102 3.880
  nonbonded pdb=" O   LEU B  75 "
            pdb=" OG  SER B 188 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" CE1 HIS B 323 "
            pdb=" CD1 LEU B 394 "
     model   vdw
     2.134 3.680
  ... (remaining 58889 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
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      :  0.005   0.044   7974  Z= 0.323
  Angle     :  0.736   7.694  10938  Z= 0.461
  Chirality :  0.051   0.216   1220
  Planarity :  0.027   0.487   1424
  Dihedral  : 11.019  82.193   2820
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  8.82 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.24), residues: 1010
  helix: -3.05 (0.55), residues: 51
  sheet: -0.72 (0.35), residues: 256
  loop : -2.31 (0.21), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.011   0.001   TYR B 365 
 PHE   0.011   0.001   PHE B 421 
 TRP   0.005   0.001   TRP A 346 
 HIS   0.006   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 7974)
  covalent geometry    : angle       0.73637 (10938)
  hydrogen bonds       : bond        0.18184 (  144)
  hydrogen bonds       : angle       7.84653 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7853 (ttmm)
REVERT: B  327 PHE cc_start: 0.8693 (m-80) cc_final: 0.8419 (m-80)
REVERT: B  339 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7448 (pttt)
REVERT: B  477 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8422 (p)
  outliers start: 19
  outliers final: 10
  residues processed: 157
  average time/residue: 0.0765
  time to fit residues: 15.8213
Evaluate side-chains
  99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  161 LYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  399 ASN
Chi-restraints excluded: chain A residue  505 ASP
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  477 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.114809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.085146 restraints weight = 13948.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.087893 restraints weight = 7867.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.089657 restraints weight = 5410.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.090824 restraints weight = 4211.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.091558 restraints weight = 3574.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   7974  Z= 0.208
  Angle     :  0.667   8.801  10938  Z= 0.339
  Chirality :  0.050   0.161   1220
  Planarity :  0.005   0.044   1424
  Dihedral  :  5.304  29.008   1109
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.13 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 13.76 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.25), residues: 1010
  helix: -2.52 (0.65), residues: 43
  sheet: -0.81 (0.34), residues: 264
  loop : -2.22 (0.21), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 321 
 TYR   0.017   0.002   TYR A 378 
 PHE   0.017   0.002   PHE B 327 
 TRP   0.010   0.001   TRP B 513 
 HIS   0.007   0.001   HIS B 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 7974)
  covalent geometry    : angle       0.66733 (10938)
  hydrogen bonds       : bond        0.03909 (  144)
  hydrogen bonds       : angle       6.50010 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 93
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  206 ASN cc_start: 0.6764 (t0) cc_final: 0.6497 (t0)
REVERT: B  154 ASP cc_start: 0.8338 (t70) cc_final: 0.8013 (t0)
REVERT: B  339 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7321 (pttt)
REVERT: B  477 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8439 (p)
REVERT: B  479 GLU cc_start: 0.7827 (mp0) cc_final: 0.7489 (mp0)
  outliers start: 37
  outliers final: 20
  residues processed: 127
  average time/residue: 0.0650
  time to fit residues: 11.5560
Evaluate side-chains
  99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 79 optimal weight:   20.0000
   chunk 50 optimal weight:   30.0000
   chunk 60 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0070
   chunk 7 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0980
   chunk 23 optimal weight:    4.9990
   overall best weight:    3.2204

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

Flipped N/Q/H residues before XYZ refinement:
B 156 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.085551 restraints weight = 13845.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.088300 restraints weight = 7731.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.090108 restraints weight = 5314.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.091284 restraints weight = 4150.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.091947 restraints weight = 3523.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7974  Z= 0.142
  Angle     :  0.600   7.646  10938  Z= 0.301
  Chirality :  0.048   0.162   1220
  Planarity :  0.005   0.042   1424
  Dihedral  :  5.061  27.192   1101
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 13.88 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.24), residues: 1010
  helix: -2.48 (0.59), residues: 45
  sheet: -0.79 (0.34), residues: 261
  loop : -2.16 (0.21), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 321 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.015   0.001   PHE B 272 
 TRP   0.005   0.001   TRP B 513 
 HIS   0.003   0.001   HIS B 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7974)
  covalent geometry    : angle       0.60041 (10938)
  hydrogen bonds       : bond        0.03414 (  144)
  hydrogen bonds       : angle       6.15494 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 78
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7327 (t0)
REVERT: A  372 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6767 (mp)
REVERT: B  339 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7632 (pttt)
REVERT: B  477 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (p)
REVERT: B  522 ASN cc_start: 0.9026 (t0) cc_final: 0.8688 (t0)
  outliers start: 38
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0653
  time to fit residues: 10.4636
Evaluate side-chains
  101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  396 ILE
Chi-restraints excluded: chain B residue  400 CYS
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  477 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.0050
   chunk 79 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   chunk 15 optimal weight:    0.4980
   chunk 73 optimal weight:    9.9990
   chunk 56 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0570
   chunk 94 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    2.9116

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.085410 restraints weight = 14087.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.088203 restraints weight = 7791.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.090012 restraints weight = 5318.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.091215 restraints weight = 4139.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.091974 restraints weight = 3504.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7974  Z= 0.131
  Angle     :  0.585   7.540  10938  Z= 0.291
  Chirality :  0.047   0.171   1220
  Planarity :  0.004   0.041   1424
  Dihedral  :  4.890  27.293   1099
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 14.47 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.24), residues: 1010
  helix: -2.29 (0.60), residues: 45
  sheet: -0.78 (0.33), residues: 268
  loop : -2.14 (0.21), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 286 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.015   0.001   PHE B 272 
 TRP   0.005   0.001   TRP B 513 
 HIS   0.004   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7974)
  covalent geometry    : angle       0.58472 (10938)
  hydrogen bonds       : bond        0.03067 (  144)
  hydrogen bonds       : angle       6.00428 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 82
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7180 (t0)
REVERT: A  204 GLN cc_start: 0.9046 (pp30) cc_final: 0.8558 (pp30)
REVERT: A  327 PHE cc_start: 0.8031 (m-10) cc_final: 0.7684 (m-80)
REVERT: A  372 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6874 (mt)
REVERT: A  383 MET cc_start: 0.9170 (ppp) cc_final: 0.8792 (ppp)
REVERT: B   53 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8942 (p)
REVERT: B  339 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7677 (pttt)
REVERT: B  405 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7818 (p0)
REVERT: B  477 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8437 (p)
REVERT: B  522 ASN cc_start: 0.9117 (t0) cc_final: 0.8718 (t0)
  outliers start: 42
  outliers final: 26
  residues processed: 119
  average time/residue: 0.0688
  time to fit residues: 11.4885
Evaluate side-chains
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  405 ASP
Chi-restraints excluded: chain B residue  447 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  505 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 89 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.3364

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN
B  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.085918 restraints weight = 13947.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.088682 restraints weight = 7707.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.090499 restraints weight = 5269.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.091663 restraints weight = 4114.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.092354 restraints weight = 3494.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7974  Z= 0.115
  Angle     :  0.570   7.686  10938  Z= 0.282
  Chirality :  0.047   0.161   1220
  Planarity :  0.004   0.040   1424
  Dihedral  :  4.795  27.742   1099
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 15.65 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.25), residues: 1010
  helix: -2.11 (0.62), residues: 45
  sheet: -0.69 (0.34), residues: 264
  loop : -2.09 (0.21), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 286 
 TYR   0.013   0.001   TYR A 365 
 PHE   0.016   0.001   PHE B 272 
 TRP   0.012   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7974)
  covalent geometry    : angle       0.56994 (10938)
  hydrogen bonds       : bond        0.02924 (  144)
  hydrogen bonds       : angle       5.88428 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 75
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.8145 (t80) cc_final: 0.7716 (t80)
REVERT: A  160 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7020 (t0)
REVERT: A  204 GLN cc_start: 0.9047 (pp30) cc_final: 0.8587 (pp30)
REVERT: A  372 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6481 (mt)
REVERT: A  383 MET cc_start: 0.9207 (ppp) cc_final: 0.8856 (ppp)
REVERT: B  339 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7718 (pttt)
REVERT: B  477 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8422 (p)
REVERT: B  522 ASN cc_start: 0.9192 (t0) cc_final: 0.8937 (t0)
  outliers start: 36
  outliers final: 27
  residues processed: 106
  average time/residue: 0.0831
  time to fit residues: 12.3873
Evaluate side-chains
  103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  512 SER
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 47 optimal weight:   20.0000
   chunk 86 optimal weight:   20.0000
   chunk 77 optimal weight:    0.8980
   chunk 7 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   overall best weight:    2.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.085381 restraints weight = 14037.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.088140 restraints weight = 7765.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.089953 restraints weight = 5312.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.091095 restraints weight = 4139.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.091886 restraints weight = 3527.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7974  Z= 0.124
  Angle     :  0.570   8.429  10938  Z= 0.283
  Chirality :  0.047   0.172   1220
  Planarity :  0.004   0.041   1424
  Dihedral  :  4.731  29.209   1099
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.29 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.25), residues: 1010
  helix: -2.03 (0.62), residues: 45
  sheet: -0.61 (0.34), residues: 258
  loop : -2.08 (0.21), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 164 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.014   0.001   PHE B 272 
 TRP   0.006   0.001   TRP B 346 
 HIS   0.004   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7974)
  covalent geometry    : angle       0.56958 (10938)
  hydrogen bonds       : bond        0.02865 (  144)
  hydrogen bonds       : angle       5.81568 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 77
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 PHE cc_start: 0.8270 (t80) cc_final: 0.7847 (t80)
REVERT: A  160 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7112 (t0)
REVERT: A  204 GLN cc_start: 0.9030 (pp30) cc_final: 0.8542 (pp30)
REVERT: A  372 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6379 (mt)
REVERT: A  383 MET cc_start: 0.9197 (ppp) cc_final: 0.8960 (ppp)
REVERT: B   53 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8941 (p)
REVERT: B  339 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7796 (pttt)
REVERT: B  477 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8411 (p)
REVERT: B  522 ASN cc_start: 0.9204 (t0) cc_final: 0.8944 (t0)
  outliers start: 42
  outliers final: 30
  residues processed: 114
  average time/residue: 0.0748
  time to fit residues: 12.1215
Evaluate side-chains
  107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 72
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  512 SER
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 60 optimal weight:    9.9990
   chunk 98 optimal weight:    0.0060
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.6004

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

Flipped N/Q/H residues before XYZ refinement:
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.114410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.084375 restraints weight = 14050.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.087127 restraints weight = 7819.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.088930 restraints weight = 5358.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.090084 restraints weight = 4176.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.090862 restraints weight = 3555.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7974  Z= 0.146
  Angle     :  0.576   8.924  10938  Z= 0.287
  Chirality :  0.048   0.165   1220
  Planarity :  0.004   0.040   1424
  Dihedral  :  4.803  30.564   1099
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 15.29 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.25), residues: 1010
  helix: -1.97 (0.64), residues: 45
  sheet: -0.78 (0.34), residues: 267
  loop : -2.05 (0.21), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 321 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.014   0.001   PHE B 272 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.004   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7974)
  covalent geometry    : angle       0.57595 (10938)
  hydrogen bonds       : bond        0.03023 (  144)
  hydrogen bonds       : angle       5.84159 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 71
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7310 (t0)
REVERT: A  204 GLN cc_start: 0.9034 (pp30) cc_final: 0.8500 (pp30)
REVERT: A  372 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6647 (mt)
REVERT: A  383 MET cc_start: 0.9175 (ppp) cc_final: 0.8959 (ppp)
REVERT: B   53 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.8918 (p)
REVERT: B  339 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7826 (pttt)
  outliers start: 45
  outliers final: 33
  residues processed: 107
  average time/residue: 0.0787
  time to fit residues: 11.9983
Evaluate side-chains
  104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 67
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  505 ASP
Chi-restraints excluded: chain B residue  512 SER
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 74 optimal weight:   20.0000
   chunk 56 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 54 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 16 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.081527 restraints weight = 14183.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.084190 restraints weight = 7941.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.085945 restraints weight = 5488.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.087095 restraints weight = 4311.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.087849 restraints weight = 3678.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   7974  Z= 0.225
  Angle     :  0.648   9.969  10938  Z= 0.326
  Chirality :  0.050   0.160   1220
  Planarity :  0.005   0.044   1424
  Dihedral  :  5.133  34.053   1097
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.32 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.12 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.24), residues: 1010
  helix: -2.08 (0.65), residues: 45
  sheet: -0.93 (0.33), residues: 275
  loop : -2.13 (0.21), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 225 
 TYR   0.016   0.002   TYR A 365 
 PHE   0.016   0.002   PHE B 272 
 TRP   0.013   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 7974)
  covalent geometry    : angle       0.64820 (10938)
  hydrogen bonds       : bond        0.03497 (  144)
  hydrogen bonds       : angle       6.04938 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 66
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  160 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7067 (t0)
REVERT: A  204 GLN cc_start: 0.9131 (pp30) cc_final: 0.8511 (pp30)
REVERT: A  289 MET cc_start: 0.7812 (mtp) cc_final: 0.7410 (mtp)
REVERT: A  372 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6722 (mt)
REVERT: A  383 MET cc_start: 0.9126 (ppp) cc_final: 0.8915 (ppp)
REVERT: B   53 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.8958 (p)
REVERT: B  339 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7818 (pttt)
  outliers start: 42
  outliers final: 35
  residues processed: 101
  average time/residue: 0.0833
  time to fit residues: 11.8279
Evaluate side-chains
  101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 62
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  505 ASP
Chi-restraints excluded: chain B residue  512 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:   40.0000
   chunk 91 optimal weight:   40.0000
   chunk 88 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    4.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.082766 restraints weight = 14088.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.085462 restraints weight = 7886.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.087230 restraints weight = 5441.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.088409 restraints weight = 4275.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.089091 restraints weight = 3624.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   7974  Z= 0.165
  Angle     :  0.600  10.422  10938  Z= 0.301
  Chirality :  0.048   0.162   1220
  Planarity :  0.005   0.093   1424
  Dihedral  :  5.036  33.502   1097
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.14 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 16.24 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.24), residues: 1010
  helix: -2.03 (0.65), residues: 45
  sheet: -0.83 (0.33), residues: 263
  loop : -2.12 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 286 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.015   0.001   PHE B 272 
 TRP   0.007   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7974)
  covalent geometry    : angle       0.59950 (10938)
  hydrogen bonds       : bond        0.03097 (  144)
  hydrogen bonds       : angle       5.93936 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 64
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  160 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.6932 (t0)
REVERT: A  204 GLN cc_start: 0.9081 (pp30) cc_final: 0.8560 (pp30)
REVERT: B   53 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.8927 (p)
REVERT: B  339 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7800 (pttt)
  outliers start: 42
  outliers final: 34
  residues processed: 100
  average time/residue: 0.0758
  time to fit residues: 11.0743
Evaluate side-chains
  98 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 61
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  146 ILE
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  160 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  505 ASP
Chi-restraints excluded: chain B residue  512 SER
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.114327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.084317 restraints weight = 13958.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.087063 restraints weight = 7767.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.088857 restraints weight = 5329.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.090013 restraints weight = 4170.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.090790 restraints weight = 3558.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7974  Z= 0.112
  Angle     :  0.578  11.237  10938  Z= 0.286
  Chirality :  0.047   0.170   1220
  Planarity :  0.004   0.051   1424
  Dihedral  :  4.780  31.459   1097
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 17.76 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.25), residues: 1010
  helix: -1.85 (0.65), residues: 45
  sheet: -0.81 (0.34), residues: 263
  loop : -2.05 (0.21), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 286 
 TYR   0.011   0.001   TYR A 365 
 PHE   0.016   0.001   PHE B 272 
 TRP   0.007   0.001   TRP A 285 
 HIS   0.003   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7974)
  covalent geometry    : angle       0.57836 (10938)
  hydrogen bonds       : bond        0.02747 (  144)
  hydrogen bonds       : angle       5.73371 (  369)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  204 GLN cc_start: 0.9043 (pp30) cc_final: 0.8586 (pp30)
REVERT: A  373 ASP cc_start: 0.7267 (p0) cc_final: 0.6832 (p0)
REVERT: B   53 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.8924 (p)
REVERT: B  339 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7799 (pttt)
  outliers start: 31
  outliers final: 27
  residues processed: 94
  average time/residue: 0.0741
  time to fit residues: 10.0113
Evaluate side-chains
  98 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  236 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  339 LYS
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  414 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  472 LEU
Chi-restraints excluded: chain B residue  524 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 74 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 41 optimal weight:   30.0000
   chunk 7 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0670
   chunk 33 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    5.0126

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.082147 restraints weight = 14059.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.084833 restraints weight = 7907.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.086623 restraints weight = 5472.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.087759 restraints weight = 4295.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.088534 restraints weight = 3671.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   7974  Z= 0.189
  Angle     :  0.617  10.996  10938  Z= 0.308
  Chirality :  0.048   0.168   1220
  Planarity :  0.005   0.057   1424
  Dihedral  :  4.935  33.631   1096
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.62 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 16.35 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.24), residues: 1010
  helix: -1.93 (0.65), residues: 45
  sheet: -0.86 (0.34), residues: 253
  loop : -2.02 (0.21), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 225 
 TYR   0.015   0.001   TYR A 365 
 PHE   0.015   0.002   PHE B 272 
 TRP   0.010   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 7974)
  covalent geometry    : angle       0.61661 (10938)
  hydrogen bonds       : bond        0.03203 (  144)
  hydrogen bonds       : angle       5.88586 (  369)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1186.65 seconds
wall clock time: 21 minutes 11.59 seconds (1271.59 seconds total)