Starting phenix.real_space_refine
on Wed Mar  4 14:50:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zvp_11467/03_2026/6zvp_11467.cif"
  }
  resolution = 4.0
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      40      5.16       5
     C    9232      2.51       5
     N    2532      2.21       5
     O    2744      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14552
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 3626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3626
          Classifications: {'peptide': 458}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 429}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {' FE': 1, 'LDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    A, B, C
  Time building chain proxies: 2.74, per 1000 atoms: 0.19
  Number of scatterers: 14552
  At special positions: 0
  Unit cell: (106.05, 131.25, 120.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      40     16.00
     O    2744      8.00
     N    2532      7.00
     C    9232      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 692.6 milliseconds
  

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3472

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 18 sheets defined
      51.4% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'D' and resid 40 through 58
    Processing helix  chain 'D' and resid 95 through 104
      removed outlier: 3.676A  pdb=" N   ALA D  99 " --> pdb=" O   ALA D  95 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU D 104 " --> pdb=" O   VAL D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 107
      No H-bonds generated for 'chain 'D' and resid 105 through 107'
    Processing helix  chain 'D' and resid 138 through 149
      removed outlier: 4.134A  pdb=" N   ALA D 142 " --> pdb=" O   ARG D 138 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA D 143 " --> pdb=" O   GLY D 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY D 147 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 180
      removed outlier: 3.736A  pdb=" N   HIS D 177 " --> pdb=" O   LEU D 173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 212
    Processing helix  chain 'D' and resid 225 through 244
      removed outlier: 3.680A  pdb=" N   LEU D 242 " --> pdb=" O   THR D 238 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA D 244 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 262
    Processing helix  chain 'D' and resid 272 through 283
    Processing helix  chain 'D' and resid 295 through 305
      removed outlier: 3.923A  pdb=" N   PHE D 299 " --> pdb=" O   SER D 295 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 334
    Processing helix  chain 'D' and resid 335 through 340
    Processing helix  chain 'D' and resid 341 through 356
    Processing helix  chain 'D' and resid 359 through 374
    Processing helix  chain 'D' and resid 395 through 403
      removed outlier: 3.991A  pdb=" N   LEU D 403 " --> pdb=" O   LEU D 399 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 413 through 420
    Processing helix  chain 'D' and resid 436 through 451
    Processing helix  chain 'D' and resid 471 through 496
      removed outlier: 3.728A  pdb=" N   VAL D 475 " --> pdb=" O   SER D 471 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY D 481 " --> pdb=" O   ARG D 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 58
    Processing helix  chain 'A' and resid 95 through 104
      removed outlier: 3.676A  pdb=" N   ALA A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 107
      No H-bonds generated for 'chain 'A' and resid 105 through 107'
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 4.134A  pdb=" N   ALA A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY A 147 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 180
      removed outlier: 3.736A  pdb=" N   HIS A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 212
    Processing helix  chain 'A' and resid 225 through 244
      removed outlier: 3.680A  pdb=" N   LEU A 242 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA A 244 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.923A  pdb=" N   PHE A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 334
    Processing helix  chain 'A' and resid 335 through 340
    Processing helix  chain 'A' and resid 341 through 356
    Processing helix  chain 'A' and resid 359 through 374
    Processing helix  chain 'A' and resid 395 through 403
      removed outlier: 3.991A  pdb=" N   LEU A 403 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 420
    Processing helix  chain 'A' and resid 436 through 451
    Processing helix  chain 'A' and resid 471 through 496
      removed outlier: 3.728A  pdb=" N   VAL A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 481 " --> pdb=" O   ARG A 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 58
    Processing helix  chain 'B' and resid 95 through 104
      removed outlier: 3.676A  pdb=" N   ALA B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU B 104 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 4.134A  pdb=" N   ALA B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA B 143 " --> pdb=" O   GLY B 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY B 147 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 180
      removed outlier: 3.736A  pdb=" N   HIS B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 212
    Processing helix  chain 'B' and resid 225 through 244
      removed outlier: 3.680A  pdb=" N   LEU B 242 " --> pdb=" O   THR B 238 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA B 244 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 262
    Processing helix  chain 'B' and resid 272 through 283
    Processing helix  chain 'B' and resid 295 through 305
      removed outlier: 3.923A  pdb=" N   PHE B 299 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 334
    Processing helix  chain 'B' and resid 335 through 340
    Processing helix  chain 'B' and resid 341 through 356
    Processing helix  chain 'B' and resid 359 through 374
    Processing helix  chain 'B' and resid 395 through 403
      removed outlier: 3.991A  pdb=" N   LEU B 403 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 420
    Processing helix  chain 'B' and resid 436 through 451
    Processing helix  chain 'B' and resid 471 through 496
      removed outlier: 3.728A  pdb=" N   VAL B 475 " --> pdb=" O   SER B 471 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY B 481 " --> pdb=" O   ARG B 477 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 58
    Processing helix  chain 'C' and resid 95 through 104
      removed outlier: 3.676A  pdb=" N   ALA C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU C 104 " --> pdb=" O   VAL C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 107
      No H-bonds generated for 'chain 'C' and resid 105 through 107'
    Processing helix  chain 'C' and resid 138 through 149
      removed outlier: 4.134A  pdb=" N   ALA C 142 " --> pdb=" O   ARG C 138 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA C 143 " --> pdb=" O   GLY C 139 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY C 147 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 180
      removed outlier: 3.736A  pdb=" N   HIS C 177 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 212
    Processing helix  chain 'C' and resid 225 through 244
      removed outlier: 3.680A  pdb=" N   LEU C 242 " --> pdb=" O   THR C 238 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA C 244 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 262
    Processing helix  chain 'C' and resid 272 through 283
    Processing helix  chain 'C' and resid 295 through 305
      removed outlier: 3.923A  pdb=" N   PHE C 299 " --> pdb=" O   SER C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 334
    Processing helix  chain 'C' and resid 335 through 340
    Processing helix  chain 'C' and resid 341 through 356
    Processing helix  chain 'C' and resid 359 through 374
    Processing helix  chain 'C' and resid 395 through 403
      removed outlier: 3.991A  pdb=" N   LEU C 403 " --> pdb=" O   LEU C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 413 through 420
    Processing helix  chain 'C' and resid 436 through 451
    Processing helix  chain 'C' and resid 471 through 496
      removed outlier: 3.728A  pdb=" N   VAL C 475 " --> pdb=" O   SER C 471 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY C 481 " --> pdb=" O   ARG C 477 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 73 through 76
      removed outlier: 6.759A  pdb=" N   ARG D 133 " --> pdb=" O   HIS D 111 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ARG C 133 " --> pdb=" O   HIS C 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 286 through 289
      removed outlier: 6.804A  pdb=" N   GLN D 286 " --> pdb=" O   PHE D 308 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   CYS D 310 " --> pdb=" O   GLN D 286 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ARG D 288 " --> pdb=" O   CYS D 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 378 through 381
    Processing sheet with id=AA4, first strand: chain 'D' and resid 408 through 411
    Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 460
    Processing sheet with id=AA6, first strand: chain 'A' and resid 73 through 76
      removed outlier: 6.759A  pdb=" N   ARG A 133 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   ARG B 133 " --> pdb=" O   HIS B 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 286 through 289
      removed outlier: 6.803A  pdb=" N   GLN A 286 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   CYS A 310 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ARG A 288 " --> pdb=" O   CYS A 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 381
    Processing sheet with id=AA9, first strand: chain 'A' and resid 408 through 411
    Processing sheet with id=AB1, first strand: chain 'A' and resid 456 through 460
    Processing sheet with id=AB2, first strand: chain 'B' and resid 286 through 289
      removed outlier: 6.804A  pdb=" N   GLN B 286 " --> pdb=" O   PHE B 308 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   CYS B 310 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ARG B 288 " --> pdb=" O   CYS B 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 381
    Processing sheet with id=AB4, first strand: chain 'B' and resid 408 through 411
    Processing sheet with id=AB5, first strand: chain 'B' and resid 456 through 460
    Processing sheet with id=AB6, first strand: chain 'C' and resid 286 through 289
      removed outlier: 6.803A  pdb=" N   GLN C 286 " --> pdb=" O   PHE C 308 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   CYS C 310 " --> pdb=" O   GLN C 286 " (cutoff:3.500A)
      removed outlier: 6.030A  pdb=" N   ARG C 288 " --> pdb=" O   CYS C 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 378 through 381
    Processing sheet with id=AB8, first strand: chain 'C' and resid 408 through 411
    Processing sheet with id=AB9, first strand: chain 'C' and resid 456 through 460

    713 hydrogen bonds defined for protein.
    2079 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.64 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: 4892
        1.34 -     1.46: 3290
        1.46 -     1.58: 6670
        1.58 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 14904
  Sorted by residual:
  bond pdb=" C3  LDP B 502 "
       pdb=" O1  LDP B 502 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" C3  LDP D 502 "
       pdb=" O1  LDP D 502 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" C3  LDP A 502 "
       pdb=" O1  LDP A 502 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" C3  LDP C 502 "
       pdb=" O1  LDP C 502 "
    ideal  model  delta    sigma   weight residual
    1.353  1.400 -0.047 2.00e-02 2.50e+03 5.45e+00
  bond pdb=" C4  LDP D 502 "
       pdb=" O2  LDP D 502 "
    ideal  model  delta    sigma   weight residual
    1.355  1.399 -0.044 2.00e-02 2.50e+03 4.94e+00
  ... (remaining 14899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 19908
        2.08 -     4.16: 264
        4.16 -     6.24: 28
        6.24 -     8.31: 0
        8.31 -    10.39: 4
  Bond angle restraints: 20204
  Sorted by residual:
  angle pdb=" C   VAL C 336 "
        pdb=" CA  VAL C 336 "
        pdb=" CB  VAL C 336 "
      ideal   model   delta    sigma   weight residual
     113.70  110.24    3.46 9.50e-01 1.11e+00 1.33e+01
  angle pdb=" C   VAL A 336 "
        pdb=" CA  VAL A 336 "
        pdb=" CB  VAL A 336 "
      ideal   model   delta    sigma   weight residual
     113.70  110.24    3.46 9.50e-01 1.11e+00 1.33e+01
  angle pdb=" C   VAL B 336 "
        pdb=" CA  VAL B 336 "
        pdb=" CB  VAL B 336 "
      ideal   model   delta    sigma   weight residual
     113.70  110.30    3.40 9.50e-01 1.11e+00 1.28e+01
  angle pdb=" C   VAL D 336 "
        pdb=" CA  VAL D 336 "
        pdb=" CB  VAL D 336 "
      ideal   model   delta    sigma   weight residual
     113.70  110.30    3.40 9.50e-01 1.11e+00 1.28e+01
  angle pdb=" C   HIS D 335 "
        pdb=" N   VAL D 336 "
        pdb=" CA  VAL D 336 "
      ideal   model   delta    sigma   weight residual
     120.43  123.38   -2.95 9.60e-01 1.09e+00 9.47e+00
  ... (remaining 20199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.74: 8082
       13.74 -    27.49: 602
       27.49 -    41.23: 236
       41.23 -    54.97: 72
       54.97 -    68.72: 20
  Dihedral angle restraints: 9012
    sinusoidal: 3648
      harmonic: 5364
  Sorted by residual:
  dihedral pdb=" CA  HIS B 177 "
           pdb=" C   HIS B 177 "
           pdb=" N   HIS B 178 "
           pdb=" CA  HIS B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.42   18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  HIS D 177 "
           pdb=" C   HIS D 177 "
           pdb=" N   HIS D 178 "
           pdb=" CA  HIS D 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.42   18.58     0      5.00e+00 4.00e-02 1.38e+01
  dihedral pdb=" CA  HIS C 177 "
           pdb=" C   HIS C 177 "
           pdb=" N   HIS C 178 "
           pdb=" CA  HIS C 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.48   18.52     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 9009 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1316
       0.025 -    0.049: 494
       0.049 -    0.074: 214
       0.074 -    0.099: 106
       0.099 -    0.123: 42
  Chirality restraints: 2172
  Sorted by residual:
  chirality pdb=" CA  VAL A 132 "
            pdb=" N   VAL A 132 "
            pdb=" C   VAL A 132 "
            pdb=" CB  VAL A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  VAL C 132 "
            pdb=" N   VAL C 132 "
            pdb=" C   VAL C 132 "
            pdb=" CB  VAL C 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  chirality pdb=" CA  VAL D 132 "
            pdb=" N   VAL D 132 "
            pdb=" C   VAL D 132 "
            pdb=" CB  VAL D 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.61e-01
  ... (remaining 2169 not shown)

  Planarity restraints: 2676
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 125 "   -0.046 5.00e-02 4.00e+02   6.94e-02 7.70e+00
        pdb=" N   PRO D 126 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO D 126 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO D 126 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 125 "    0.046 5.00e-02 4.00e+02   6.94e-02 7.70e+00
        pdb=" N   PRO B 126 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO B 126 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 126 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 125 "    0.046 5.00e-02 4.00e+02   6.91e-02 7.65e+00
        pdb=" N   PRO A 126 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO A 126 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 126 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2673 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.38: 116
        2.38 -     3.01: 8771
        3.01 -     3.64: 24857
        3.64 -     4.27: 34588
        4.27 -     4.90: 54242
  Nonbonded interactions: 122574
  Sorted by model distance:
  nonbonded pdb=" CE1 HIS C 330 "
            pdb="FE    FE C 501 "
     model   vdw
     1.744 2.480
  nonbonded pdb=" CE1 HIS B 330 "
            pdb="FE    FE B 501 "
     model   vdw
     1.744 2.480
  nonbonded pdb=" CE1 HIS D 330 "
            pdb="FE    FE D 501 "
     model   vdw
     1.744 2.480
  nonbonded pdb=" CE1 HIS A 330 "
            pdb="FE    FE A 501 "
     model   vdw
     1.744 2.480
  nonbonded pdb=" OE2 GLU A 375 "
            pdb=" O2  LDP A 502 "
     model   vdw
     2.008 3.040
  ... (remaining 122569 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.84
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:             0.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.230
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6014
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      :  0.004   0.146  14908  Z= 0.280
  Angle     :  0.610  10.393  20204  Z= 0.347
  Chirality :  0.037   0.123   2172
  Planarity :  0.005   0.069   2676
  Dihedral  : 12.579  68.716   5540
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 10.05 %
    Favored  : 84.07 %
  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: -0.21 (0.21), residues: 1824
  helix:  1.07 (0.18), residues: 896
  sheet: -1.68 (0.51), residues: 104
  loop : -1.29 (0.22), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 297 
 TYR   0.010   0.001   TYR D 370 
 PHE   0.008   0.001   PHE A 347 
 TRP   0.014   0.002   TRP C 371 
 HIS   0.002   0.000   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (14904)
  covalent geometry    : angle       0.61023 (20204)
  hydrogen bonds       : bond        0.15746 (  713)
  hydrogen bonds       : angle       5.96552 ( 2079)
  Misc. bond           : bond        0.14605 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  574 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 484
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  219 ILE cc_start: 0.9325 (mm) cc_final: 0.9045 (mt)
REVERT: D  321 MET cc_start: 0.8919 (pmm) cc_final: 0.8331 (pmm)
REVERT: D  451 ILE cc_start: 0.9029 (mt) cc_final: 0.8827 (mm)
REVERT: A  219 ILE cc_start: 0.9323 (mm) cc_final: 0.9046 (mt)
REVERT: A  321 MET cc_start: 0.8923 (pmm) cc_final: 0.8333 (pmm)
REVERT: A  451 ILE cc_start: 0.9024 (mt) cc_final: 0.8823 (mm)
REVERT: B  219 ILE cc_start: 0.9324 (mm) cc_final: 0.9047 (mt)
REVERT: B  321 MET cc_start: 0.8922 (pmm) cc_final: 0.8335 (pmm)
REVERT: B  451 ILE cc_start: 0.9025 (mt) cc_final: 0.8823 (mm)
REVERT: C  219 ILE cc_start: 0.9325 (mm) cc_final: 0.9049 (mt)
REVERT: C  321 MET cc_start: 0.8924 (pmm) cc_final: 0.8337 (pmm)
REVERT: C  451 ILE cc_start: 0.9033 (mt) cc_final: 0.8831 (mm)
  outliers start: 90
  outliers final: 24
  residues processed: 566
  average time/residue: 0.1374
  time to fit residues: 108.8844
Evaluate side-chains
  395 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 371
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  151 VAL
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  151 VAL
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  430 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    0.0170
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.0770
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    0.0040
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
D 246 HIS
D 346 GLN
D 428 GLN
A 246 HIS
A 346 GLN
A 428 GLN
B 246 HIS
B 346 GLN
B 428 GLN
C 246 HIS
C 346 GLN
C 428 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.114431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.086325 restraints weight = 34752.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.089428 restraints weight = 23472.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.091875 restraints weight = 17467.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.093493 restraints weight = 13800.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.095109 restraints weight = 11547.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6769
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14908  Z= 0.175
  Angle     :  0.761   9.935  20204  Z= 0.375
  Chirality :  0.045   0.164   2172
  Planarity :  0.006   0.069   2676
  Dihedral  :  6.582  68.285   2068
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 19.58 %
    Favored  : 77.15 %
  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: -0.85 (0.20), residues: 1824
  helix:  0.34 (0.17), residues: 916
  sheet: -2.44 (0.36), residues: 176
  loop : -1.12 (0.24), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 288 
 TYR   0.016   0.002   TYR B 130 
 PHE   0.019   0.002   PHE C 278 
 TRP   0.009   0.003   TRP D 371 
 HIS   0.005   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14904)
  covalent geometry    : angle       0.76064 (20204)
  hydrogen bonds       : bond        0.04284 (  713)
  hydrogen bonds       : angle       5.54626 ( 2079)
  Misc. bond           : bond        0.00104 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 384
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  219 ILE cc_start: 0.9184 (mm) cc_final: 0.8699 (mt)
REVERT: D  221 ARG cc_start: 0.8626 (mmt90) cc_final: 0.7846 (mmp80)
REVERT: D  227 GLU cc_start: 0.9352 (mp0) cc_final: 0.9083 (mp0)
REVERT: D  273 GLU cc_start: 0.8734 (tp30) cc_final: 0.8412 (pm20)
REVERT: D  287 LEU cc_start: 0.9490 (mm) cc_final: 0.9256 (mm)
REVERT: D  288 ARG cc_start: 0.8328 (ttt90) cc_final: 0.7788 (ttt180)
REVERT: D  338 MET cc_start: 0.9236 (mmm) cc_final: 0.8987 (mmm)
REVERT: D  393 LEU cc_start: 0.9589 (mp) cc_final: 0.9370 (mp)
REVERT: D  396 TYR cc_start: 0.8907 (p90) cc_final: 0.8700 (p90)
REVERT: D  460 ASP cc_start: 0.9011 (t0) cc_final: 0.8781 (t0)
REVERT: D  466 ILE cc_start: 0.9195 (mm) cc_final: 0.8968 (mm)
REVERT: A  219 ILE cc_start: 0.9180 (mm) cc_final: 0.8695 (mt)
REVERT: A  221 ARG cc_start: 0.8465 (mmt90) cc_final: 0.7857 (mmp80)
REVERT: A  227 GLU cc_start: 0.9355 (mp0) cc_final: 0.9085 (mp0)
REVERT: A  273 GLU cc_start: 0.8852 (tp30) cc_final: 0.8426 (pm20)
REVERT: A  287 LEU cc_start: 0.9482 (mm) cc_final: 0.9249 (mm)
REVERT: A  288 ARG cc_start: 0.8324 (ttt90) cc_final: 0.7987 (ttt90)
REVERT: A  338 MET cc_start: 0.9237 (mmm) cc_final: 0.9009 (mmm)
REVERT: A  393 LEU cc_start: 0.9588 (mp) cc_final: 0.9371 (mp)
REVERT: A  396 TYR cc_start: 0.8923 (p90) cc_final: 0.8721 (p90)
REVERT: A  460 ASP cc_start: 0.9007 (t0) cc_final: 0.8780 (t0)
REVERT: A  466 ILE cc_start: 0.9194 (mm) cc_final: 0.8969 (mm)
REVERT: B  219 ILE cc_start: 0.9182 (mm) cc_final: 0.8688 (mt)
REVERT: B  221 ARG cc_start: 0.8492 (mmt90) cc_final: 0.7848 (mmp80)
REVERT: B  227 GLU cc_start: 0.9348 (mp0) cc_final: 0.9079 (mp0)
REVERT: B  273 GLU cc_start: 0.8862 (tp30) cc_final: 0.8428 (pm20)
REVERT: B  287 LEU cc_start: 0.9487 (mm) cc_final: 0.9254 (mm)
REVERT: B  288 ARG cc_start: 0.8326 (ttt90) cc_final: 0.7780 (ttt180)
REVERT: B  338 MET cc_start: 0.9248 (mmm) cc_final: 0.8996 (mmm)
REVERT: B  393 LEU cc_start: 0.9586 (mp) cc_final: 0.9367 (mp)
REVERT: B  396 TYR cc_start: 0.8929 (p90) cc_final: 0.8729 (p90)
REVERT: B  460 ASP cc_start: 0.9020 (t0) cc_final: 0.8790 (t0)
REVERT: B  466 ILE cc_start: 0.9190 (mm) cc_final: 0.8966 (mm)
REVERT: C  219 ILE cc_start: 0.9182 (mm) cc_final: 0.8683 (mt)
REVERT: C  221 ARG cc_start: 0.8470 (mmt90) cc_final: 0.7850 (mmp80)
REVERT: C  227 GLU cc_start: 0.9351 (mp0) cc_final: 0.9082 (mp0)
REVERT: C  273 GLU cc_start: 0.8866 (tp30) cc_final: 0.8428 (pm20)
REVERT: C  287 LEU cc_start: 0.9486 (mm) cc_final: 0.9258 (mm)
REVERT: C  288 ARG cc_start: 0.8331 (ttt90) cc_final: 0.7994 (ttt90)
REVERT: C  338 MET cc_start: 0.9244 (mmm) cc_final: 0.9017 (mmm)
REVERT: C  393 LEU cc_start: 0.9587 (mp) cc_final: 0.9371 (mp)
REVERT: C  396 TYR cc_start: 0.8920 (p90) cc_final: 0.8717 (p90)
REVERT: C  460 ASP cc_start: 0.9009 (t0) cc_final: 0.8784 (t0)
REVERT: C  466 ILE cc_start: 0.9191 (mm) cc_final: 0.8965 (mm)
  outliers start: 50
  outliers final: 24
  residues processed: 418
  average time/residue: 0.1233
  time to fit residues: 74.5639
Evaluate side-chains
  358 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 334
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain D residue  489 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  484 ASP
Chi-restraints excluded: chain C residue  489 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 173 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 161 optimal weight:    3.9990
   chunk 90 optimal weight:   30.0000
   chunk 64 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 170 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
D 483 GLN
A 483 GLN
B 483 GLN
C 483 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.111166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.084283 restraints weight = 36265.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.087266 restraints weight = 24304.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.089506 restraints weight = 18059.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.091226 restraints weight = 14334.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.092610 restraints weight = 11908.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6849
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14908  Z= 0.172
  Angle     :  0.719   8.471  20204  Z= 0.358
  Chirality :  0.044   0.173   2172
  Planarity :  0.005   0.063   2676
  Dihedral  :  5.911  59.511   2052
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.26 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.19), residues: 1824
  helix:  0.23 (0.17), residues: 916
  sheet: -2.50 (0.37), residues: 152
  loop : -1.30 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 288 
 TYR   0.016   0.002   TYR A 370 
 PHE   0.018   0.002   PHE D 278 
 TRP   0.010   0.002   TRP D 371 
 HIS   0.009   0.002   HIS D 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (14904)
  covalent geometry    : angle       0.71872 (20204)
  hydrogen bonds       : bond        0.04105 (  713)
  hydrogen bonds       : angle       5.48278 ( 2079)
  Misc. bond           : bond        0.00105 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 354
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  287 LEU cc_start: 0.9506 (mm) cc_final: 0.9271 (mm)
REVERT: D  321 MET cc_start: 0.8969 (pmm) cc_final: 0.8639 (pmm)
REVERT: D  338 MET cc_start: 0.9227 (mmm) cc_final: 0.8906 (mmm)
REVERT: D  396 TYR cc_start: 0.8909 (p90) cc_final: 0.8628 (p90)
REVERT: D  441 LYS cc_start: 0.9578 (tmtt) cc_final: 0.9322 (tptp)
REVERT: D  480 GLU cc_start: 0.8916 (tp30) cc_final: 0.8668 (tp30)
REVERT: D  491 HIS cc_start: 0.9058 (m-70) cc_final: 0.8827 (m90)
REVERT: A  287 LEU cc_start: 0.9504 (mm) cc_final: 0.9267 (mm)
REVERT: A  321 MET cc_start: 0.8975 (pmm) cc_final: 0.8655 (pmm)
REVERT: A  338 MET cc_start: 0.9223 (mmm) cc_final: 0.8905 (mmm)
REVERT: A  396 TYR cc_start: 0.8917 (p90) cc_final: 0.8640 (p90)
REVERT: A  441 LYS cc_start: 0.9583 (tmtt) cc_final: 0.9322 (tptp)
REVERT: A  480 GLU cc_start: 0.8917 (tp30) cc_final: 0.8670 (tp30)
REVERT: A  491 HIS cc_start: 0.9047 (m-70) cc_final: 0.8810 (m90)
REVERT: B  269 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: B  287 LEU cc_start: 0.9502 (mm) cc_final: 0.9262 (mm)
REVERT: B  321 MET cc_start: 0.8973 (pmm) cc_final: 0.8648 (pmm)
REVERT: B  338 MET cc_start: 0.9234 (mmm) cc_final: 0.8918 (mmm)
REVERT: B  396 TYR cc_start: 0.8915 (p90) cc_final: 0.8639 (p90)
REVERT: B  441 LYS cc_start: 0.9577 (tmtt) cc_final: 0.9321 (tptp)
REVERT: B  480 GLU cc_start: 0.8918 (tp30) cc_final: 0.8671 (tp30)
REVERT: B  491 HIS cc_start: 0.9056 (m-70) cc_final: 0.8824 (m90)
REVERT: C  287 LEU cc_start: 0.9502 (mm) cc_final: 0.9262 (mm)
REVERT: C  321 MET cc_start: 0.8968 (pmm) cc_final: 0.8646 (pmm)
REVERT: C  338 MET cc_start: 0.9239 (mmm) cc_final: 0.8921 (mmm)
REVERT: C  396 TYR cc_start: 0.8918 (p90) cc_final: 0.8641 (p90)
REVERT: C  441 LYS cc_start: 0.9577 (tmtt) cc_final: 0.9313 (tptp)
REVERT: C  480 GLU cc_start: 0.8915 (tp30) cc_final: 0.8667 (tp30)
REVERT: C  491 HIS cc_start: 0.9055 (m-70) cc_final: 0.8819 (m90)
  outliers start: 55
  outliers final: 31
  residues processed: 393
  average time/residue: 0.1057
  time to fit residues: 61.9413
Evaluate side-chains
  326 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 294
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  311 THR
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  311 THR
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  484 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 130 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 164 optimal weight:    4.9990
   chunk 8 optimal weight:   20.0000
   chunk 147 optimal weight:    0.6980
   chunk 173 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 93 optimal weight:    0.0570
   overall best weight:    0.6502

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.114011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.085207 restraints weight = 35925.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.088222 restraints weight = 24258.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.090622 restraints weight = 18087.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.092497 restraints weight = 14340.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.093918 restraints weight = 11902.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  14908  Z= 0.132
  Angle     :  0.705   9.276  20204  Z= 0.345
  Chirality :  0.044   0.163   2172
  Planarity :  0.005   0.062   2676
  Dihedral  :  5.779  57.649   2052
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.80 %
    Favored  : 75.39 %
  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: -0.83 (0.20), residues: 1824
  helix:  0.35 (0.17), residues: 912
  sheet: -2.50 (0.38), residues: 152
  loop : -1.15 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 445 
 TYR   0.014   0.002   TYR A 130 
 PHE   0.019   0.002   PHE A 183 
 TRP   0.011   0.002   TRP D 371 
 HIS   0.012   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (14904)
  covalent geometry    : angle       0.70470 (20204)
  hydrogen bonds       : bond        0.03749 (  713)
  hydrogen bonds       : angle       5.24887 ( 2079)
  Misc. bond           : bond        0.00114 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 353
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  285 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8351 (t80)
REVERT: D  321 MET cc_start: 0.8948 (pmm) cc_final: 0.8613 (pmm)
REVERT: D  338 MET cc_start: 0.9169 (mmm) cc_final: 0.8867 (mmm)
REVERT: D  396 TYR cc_start: 0.8907 (p90) cc_final: 0.8625 (p90)
REVERT: D  432 PHE cc_start: 0.9048 (m-80) cc_final: 0.8486 (m-80)
REVERT: D  441 LYS cc_start: 0.9650 (tmtt) cc_final: 0.9290 (tptp)
REVERT: D  445 ARG cc_start: 0.9296 (tpp-160) cc_final: 0.8971 (tpp80)
REVERT: A  321 MET cc_start: 0.8947 (pmm) cc_final: 0.8617 (pmm)
REVERT: A  338 MET cc_start: 0.9173 (mmm) cc_final: 0.8873 (mmm)
REVERT: A  396 TYR cc_start: 0.8915 (p90) cc_final: 0.8644 (p90)
REVERT: A  432 PHE cc_start: 0.9050 (m-80) cc_final: 0.8491 (m-80)
REVERT: A  441 LYS cc_start: 0.9651 (tmtt) cc_final: 0.9301 (tptp)
REVERT: A  445 ARG cc_start: 0.9301 (tpp-160) cc_final: 0.8975 (tpp80)
REVERT: B  321 MET cc_start: 0.8958 (pmm) cc_final: 0.8626 (pmm)
REVERT: B  338 MET cc_start: 0.9182 (mmm) cc_final: 0.8880 (mmm)
REVERT: B  396 TYR cc_start: 0.8911 (p90) cc_final: 0.8632 (p90)
REVERT: B  432 PHE cc_start: 0.9059 (m-80) cc_final: 0.8488 (m-80)
REVERT: B  441 LYS cc_start: 0.9651 (tmtt) cc_final: 0.9296 (tptp)
REVERT: B  445 ARG cc_start: 0.9294 (tpp-160) cc_final: 0.8973 (tpp80)
REVERT: C  321 MET cc_start: 0.8941 (pmm) cc_final: 0.8609 (pmm)
REVERT: C  338 MET cc_start: 0.9186 (mmm) cc_final: 0.8886 (mmm)
REVERT: C  396 TYR cc_start: 0.8913 (p90) cc_final: 0.8642 (p90)
REVERT: C  432 PHE cc_start: 0.9060 (m-80) cc_final: 0.8492 (m-80)
REVERT: C  441 LYS cc_start: 0.9645 (tmtt) cc_final: 0.9290 (tptp)
REVERT: C  445 ARG cc_start: 0.9301 (tpp-160) cc_final: 0.8978 (tpp80)
  outliers start: 43
  outliers final: 24
  residues processed: 382
  average time/residue: 0.1036
  time to fit residues: 60.4847
Evaluate side-chains
  345 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 320
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0470
   chunk 3 optimal weight:    6.9990
   chunk 34 optimal weight:    0.2980
   chunk 72 optimal weight:    6.9990
   chunk 108 optimal weight:    8.9990
   chunk 96 optimal weight:    6.9990
   chunk 139 optimal weight:   20.0000
   chunk 130 optimal weight:    2.9990
   chunk 143 optimal weight:   20.0000
   chunk 16 optimal weight:    5.9990
   overall best weight:    2.8684

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

Flipped N/Q/H residues before XYZ refinement:
D 312 GLN
A 312 GLN
B 312 GLN
C 312 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.111049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.082202 restraints weight = 38284.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.085096 restraints weight = 25557.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.087371 restraints weight = 18969.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.089177 restraints weight = 15050.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.090488 restraints weight = 12485.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  14908  Z= 0.169
  Angle     :  0.714  13.068  20204  Z= 0.344
  Chirality :  0.044   0.174   2172
  Planarity :  0.005   0.055   2676
  Dihedral  :  5.592  54.887   2052
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.93 %
    Favored  : 75.46 %
  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: -0.79 (0.20), residues: 1824
  helix:  0.30 (0.17), residues: 912
  sheet: -2.39 (0.39), residues: 144
  loop : -1.06 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 445 
 TYR   0.015   0.002   TYR B 313 
 PHE   0.014   0.002   PHE B 278 
 TRP   0.010   0.002   TRP B 232 
 HIS   0.017   0.002   HIS D 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14904)
  covalent geometry    : angle       0.71371 (20204)
  hydrogen bonds       : bond        0.03796 (  713)
  hydrogen bonds       : angle       5.26941 ( 2079)
  Misc. bond           : bond        0.00064 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 354
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  285 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8613 (t80)
REVERT: D  309 GLN cc_start: 0.9224 (mm-40) cc_final: 0.9019 (mm-40)
REVERT: D  321 MET cc_start: 0.9000 (pmm) cc_final: 0.8703 (pmm)
REVERT: D  338 MET cc_start: 0.9281 (mmm) cc_final: 0.9004 (mmm)
REVERT: D  344 PHE cc_start: 0.9560 (t80) cc_final: 0.9330 (t80)
REVERT: D  356 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8634 (mm)
REVERT: D  396 TYR cc_start: 0.8895 (p90) cc_final: 0.8628 (p90)
REVERT: D  441 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9308 (tptp)
REVERT: D  445 ARG cc_start: 0.9305 (tpp-160) cc_final: 0.9067 (tpp80)
REVERT: A  251 HIS cc_start: 0.9382 (t70) cc_final: 0.9168 (t70)
REVERT: A  285 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8630 (t80)
REVERT: A  321 MET cc_start: 0.8995 (pmm) cc_final: 0.8692 (pmm)
REVERT: A  344 PHE cc_start: 0.9558 (t80) cc_final: 0.9335 (t80)
REVERT: A  356 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8640 (mm)
REVERT: A  396 TYR cc_start: 0.8878 (p90) cc_final: 0.8610 (p90)
REVERT: A  441 LYS cc_start: 0.9648 (tmtt) cc_final: 0.9090 (tptp)
REVERT: A  445 ARG cc_start: 0.9316 (tpp-160) cc_final: 0.8822 (tpp80)
REVERT: A  491 HIS cc_start: 0.9023 (m90) cc_final: 0.8734 (m90)
REVERT: B  251 HIS cc_start: 0.9416 (t70) cc_final: 0.9189 (t70)
REVERT: B  285 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8627 (t80)
REVERT: B  321 MET cc_start: 0.8987 (pmm) cc_final: 0.8686 (pmm)
REVERT: B  344 PHE cc_start: 0.9563 (t80) cc_final: 0.9340 (t80)
REVERT: B  356 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8629 (mm)
REVERT: B  396 TYR cc_start: 0.8884 (p90) cc_final: 0.8616 (p90)
REVERT: B  441 LYS cc_start: 0.9648 (tmtt) cc_final: 0.9315 (tptp)
REVERT: B  445 ARG cc_start: 0.9309 (tpp-160) cc_final: 0.9074 (tpp80)
REVERT: C  251 HIS cc_start: 0.9384 (t70) cc_final: 0.9159 (t70)
REVERT: C  285 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8627 (t80)
REVERT: C  321 MET cc_start: 0.8997 (pmm) cc_final: 0.8700 (pmm)
REVERT: C  344 PHE cc_start: 0.9564 (t80) cc_final: 0.9341 (t80)
REVERT: C  356 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8621 (mm)
REVERT: C  396 TYR cc_start: 0.8890 (p90) cc_final: 0.8623 (p90)
REVERT: C  432 PHE cc_start: 0.9186 (m-80) cc_final: 0.8504 (m-80)
REVERT: C  441 LYS cc_start: 0.9643 (tmtt) cc_final: 0.9086 (tptp)
REVERT: C  445 ARG cc_start: 0.9322 (tpp-160) cc_final: 0.8825 (tpp80)
REVERT: C  491 HIS cc_start: 0.9018 (m90) cc_final: 0.8729 (m90)
  outliers start: 40
  outliers final: 28
  residues processed: 378
  average time/residue: 0.1041
  time to fit residues: 59.9571
Evaluate side-chains
  362 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 326
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  466 ILE
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  466 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 29 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 36 optimal weight:   20.0000
   chunk 168 optimal weight:    4.9990
   chunk 55 optimal weight:   30.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 312 GLN
A 271 GLN
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 GLN
C 271 GLN
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.107862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.079586 restraints weight = 39435.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.082433 restraints weight = 25869.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.084635 restraints weight = 19016.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.086301 restraints weight = 14999.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.087589 restraints weight = 12418.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  14908  Z= 0.205
  Angle     :  0.713   8.676  20204  Z= 0.356
  Chirality :  0.044   0.240   2172
  Planarity :  0.004   0.051   2676
  Dihedral  :  5.697  56.374   2052
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 23.04 %
    Favored  : 73.43 %
  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: -0.94 (0.20), residues: 1824
  helix:  0.15 (0.17), residues: 916
  sheet: -2.60 (0.38), residues: 144
  loop : -1.06 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 203 
 TYR   0.018   0.002   TYR C 313 
 PHE   0.015   0.002   PHE D 305 
 TRP   0.009   0.002   TRP B 232 
 HIS   0.016   0.002   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (14904)
  covalent geometry    : angle       0.71290 (20204)
  hydrogen bonds       : bond        0.03909 (  713)
  hydrogen bonds       : angle       5.34599 ( 2079)
  Misc. bond           : bond        0.00056 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  402 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 348
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  285 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8772 (t80)
REVERT: D  309 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8793 (mm-40)
REVERT: D  321 MET cc_start: 0.9064 (pmm) cc_final: 0.8594 (pmm)
REVERT: D  338 MET cc_start: 0.9330 (mmm) cc_final: 0.9054 (mmm)
REVERT: D  344 PHE cc_start: 0.9600 (t80) cc_final: 0.9363 (t80)
REVERT: D  356 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8718 (mm)
REVERT: D  441 LYS cc_start: 0.9630 (tmtt) cc_final: 0.9417 (tptp)
REVERT: D  445 ARG cc_start: 0.9340 (tpp-160) cc_final: 0.9108 (tpp80)
REVERT: A  251 HIS cc_start: 0.9341 (t70) cc_final: 0.9051 (t70)
REVERT: A  271 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8925 (mm-40)
REVERT: A  285 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8768 (t80)
REVERT: A  321 MET cc_start: 0.9065 (pmm) cc_final: 0.8585 (pmm)
REVERT: A  344 PHE cc_start: 0.9608 (t80) cc_final: 0.9373 (t80)
REVERT: A  356 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: A  441 LYS cc_start: 0.9633 (tmtt) cc_final: 0.9377 (tptp)
REVERT: A  491 HIS cc_start: 0.9093 (m90) cc_final: 0.8751 (m90)
REVERT: B  251 HIS cc_start: 0.9347 (t70) cc_final: 0.9051 (t70)
REVERT: B  285 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8764 (t80)
REVERT: B  321 MET cc_start: 0.9065 (pmm) cc_final: 0.8586 (pmm)
REVERT: B  344 PHE cc_start: 0.9613 (t80) cc_final: 0.9377 (t80)
REVERT: B  356 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8712 (mm)
REVERT: B  441 LYS cc_start: 0.9628 (tmtt) cc_final: 0.9411 (tptp)
REVERT: B  445 ARG cc_start: 0.9347 (tpp-160) cc_final: 0.9115 (tpp80)
REVERT: C  251 HIS cc_start: 0.9345 (t70) cc_final: 0.9052 (t70)
REVERT: C  271 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8920 (mm-40)
REVERT: C  285 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8768 (t80)
REVERT: C  321 MET cc_start: 0.9073 (pmm) cc_final: 0.8591 (pmm)
REVERT: C  344 PHE cc_start: 0.9612 (t80) cc_final: 0.9376 (t80)
REVERT: C  356 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8712 (mm)
REVERT: C  441 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9372 (tptp)
REVERT: C  491 HIS cc_start: 0.9093 (m90) cc_final: 0.8750 (m90)
  outliers start: 54
  outliers final: 38
  residues processed: 376
  average time/residue: 0.0995
  time to fit residues: 57.8766
Evaluate side-chains
  367 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 319
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  300 LEU
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  449 SER
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  271 GLN
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  271 GLN
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  449 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 0 optimal weight:   40.0000
   chunk 21 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 36 optimal weight:    0.4980
   chunk 58 optimal weight:   10.0000
   chunk 70 optimal weight:    7.9990
   chunk 163 optimal weight:   20.0000
   chunk 131 optimal weight:    0.2980
   chunk 165 optimal weight:    1.9990
   chunk 132 optimal weight:    8.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.106798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.080485 restraints weight = 37857.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.083341 restraints weight = 24822.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.085439 restraints weight = 18192.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.087107 restraints weight = 14317.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.088416 restraints weight = 11799.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14908  Z= 0.191
  Angle     :  0.728  10.986  20204  Z= 0.362
  Chirality :  0.044   0.155   2172
  Planarity :  0.004   0.050   2676
  Dihedral  :  5.782  57.964   2052
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.98 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.20), residues: 1824
  helix:  0.17 (0.17), residues: 916
  sheet: -2.74 (0.36), residues: 144
  loop : -1.04 (0.23), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 221 
 TYR   0.017   0.002   TYR D 370 
 PHE   0.013   0.002   PHE D 376 
 TRP   0.011   0.003   TRP B 371 
 HIS   0.013   0.002   HIS D 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (14904)
  covalent geometry    : angle       0.72849 (20204)
  hydrogen bonds       : bond        0.03873 (  713)
  hydrogen bonds       : angle       5.38745 ( 2079)
  Misc. bond           : bond        0.00077 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 342
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7296 (t0)
REVERT: D  285 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8796 (t80)
REVERT: D  321 MET cc_start: 0.8975 (pmm) cc_final: 0.8640 (pmm)
REVERT: D  338 MET cc_start: 0.9302 (mmm) cc_final: 0.9053 (mmm)
REVERT: D  344 PHE cc_start: 0.9611 (t80) cc_final: 0.9355 (t80)
REVERT: D  356 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8734 (mm)
REVERT: D  441 LYS cc_start: 0.9640 (tmtt) cc_final: 0.9411 (tptp)
REVERT: A  174 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7251 (t0)
REVERT: A  251 HIS cc_start: 0.9374 (t70) cc_final: 0.9096 (t70)
REVERT: A  285 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8805 (t80)
REVERT: A  321 MET cc_start: 0.8970 (pmm) cc_final: 0.8630 (pmm)
REVERT: A  338 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8654 (tpt)
REVERT: A  344 PHE cc_start: 0.9614 (t80) cc_final: 0.9272 (t80)
REVERT: A  356 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: A  441 LYS cc_start: 0.9643 (tmtt) cc_final: 0.9431 (tptp)
REVERT: A  491 HIS cc_start: 0.9141 (m-70) cc_final: 0.8837 (m90)
REVERT: B  174 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7255 (t0)
REVERT: B  251 HIS cc_start: 0.9385 (t70) cc_final: 0.9108 (t70)
REVERT: B  285 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8785 (t80)
REVERT: B  321 MET cc_start: 0.8967 (pmm) cc_final: 0.8632 (pmm)
REVERT: B  338 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8647 (tpt)
REVERT: B  344 PHE cc_start: 0.9621 (t80) cc_final: 0.9277 (t80)
REVERT: B  356 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8720 (mm)
REVERT: B  441 LYS cc_start: 0.9642 (tmtt) cc_final: 0.9415 (tptp)
REVERT: B  445 ARG cc_start: 0.9337 (tpp-160) cc_final: 0.9134 (tpp80)
REVERT: C  174 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7231 (t0)
REVERT: C  251 HIS cc_start: 0.9377 (t70) cc_final: 0.9102 (t70)
REVERT: C  285 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8799 (t80)
REVERT: C  321 MET cc_start: 0.8959 (pmm) cc_final: 0.8619 (pmm)
REVERT: C  338 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8679 (tpt)
REVERT: C  344 PHE cc_start: 0.9614 (t80) cc_final: 0.9270 (t80)
REVERT: C  356 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8723 (mm)
REVERT: C  441 LYS cc_start: 0.9643 (tmtt) cc_final: 0.9432 (tptp)
REVERT: C  491 HIS cc_start: 0.9016 (m170) cc_final: 0.8788 (m-70)
  outliers start: 62
  outliers final: 35
  residues processed: 374
  average time/residue: 0.0989
  time to fit residues: 57.4075
Evaluate side-chains
  366 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 316
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  449 SER
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  338 MET
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  484 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 110 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   chunk 157 optimal weight:    4.9990
   chunk 136 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0970
   chunk 122 optimal weight:    3.9990
   chunk 161 optimal weight:    0.8980
   chunk 125 optimal weight:    4.9990
   overall best weight:    1.9982

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

Flipped N/Q/H residues before XYZ refinement:
** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 483 GLN
** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 271 GLN
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
A 491 HIS
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 GLN
** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 271 GLN
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 483 GLN
** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.109618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.081499 restraints weight = 37810.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.084423 restraints weight = 24654.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.086706 restraints weight = 18038.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.088461 restraints weight = 14165.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.089667 restraints weight = 11700.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.5165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14908  Z= 0.144
  Angle     :  0.725   9.327  20204  Z= 0.357
  Chirality :  0.045   0.154   2172
  Planarity :  0.004   0.048   2676
  Dihedral  :  5.800  61.840   2052
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 17.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.83 %
    Favored  : 72.45 %
  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: -0.91 (0.20), residues: 1824
  helix:  0.23 (0.17), residues: 920
  sheet: -2.82 (0.35), residues: 168
  loop : -1.00 (0.24), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 445 
 TYR   0.018   0.002   TYR D 370 
 PHE   0.011   0.002   PHE A 305 
 TRP   0.015   0.003   TRP B 371 
 HIS   0.013   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14904)
  covalent geometry    : angle       0.72491 (20204)
  hydrogen bonds       : bond        0.03694 (  713)
  hydrogen bonds       : angle       5.31363 ( 2079)
  Misc. bond           : bond        0.00098 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 367
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7172 (t0)
REVERT: D  282 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8791 (tmm-80)
REVERT: D  285 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8689 (t80)
REVERT: D  321 MET cc_start: 0.8977 (pmm) cc_final: 0.8665 (pmm)
REVERT: D  338 MET cc_start: 0.9258 (mmm) cc_final: 0.8997 (mmm)
REVERT: D  344 PHE cc_start: 0.9640 (t80) cc_final: 0.9409 (t80)
REVERT: D  356 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8721 (mm)
REVERT: D  441 LYS cc_start: 0.9646 (tmtt) cc_final: 0.9227 (tptp)
REVERT: D  445 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9142 (tpp80)
REVERT: A  174 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7202 (t0)
REVERT: A  282 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8798 (tmm-80)
REVERT: A  285 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8677 (t80)
REVERT: A  321 MET cc_start: 0.8985 (pmm) cc_final: 0.8667 (pmm)
REVERT: A  356 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8714 (mm)
REVERT: A  441 LYS cc_start: 0.9665 (tmtt) cc_final: 0.9264 (tptp)
REVERT: B  174 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7188 (t0)
REVERT: B  282 ARG cc_start: 0.9177 (ttm-80) cc_final: 0.8791 (tmm-80)
REVERT: B  285 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8667 (t80)
REVERT: B  321 MET cc_start: 0.8976 (pmm) cc_final: 0.8651 (pmm)
REVERT: B  344 PHE cc_start: 0.9653 (t80) cc_final: 0.9448 (t80)
REVERT: B  356 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8712 (mm)
REVERT: B  441 LYS cc_start: 0.9624 (tmtt) cc_final: 0.9224 (tptp)
REVERT: B  445 ARG cc_start: 0.9314 (tpp-160) cc_final: 0.9040 (tpp80)
REVERT: C  174 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7201 (t0)
REVERT: C  282 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8794 (tmm-80)
REVERT: C  285 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8670 (t80)
REVERT: C  321 MET cc_start: 0.8979 (pmm) cc_final: 0.8663 (pmm)
REVERT: C  344 PHE cc_start: 0.9646 (t80) cc_final: 0.9443 (t80)
REVERT: C  356 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8712 (mm)
REVERT: C  441 LYS cc_start: 0.9664 (tmtt) cc_final: 0.9261 (tptp)
  outliers start: 57
  outliers final: 31
  residues processed: 403
  average time/residue: 0.1003
  time to fit residues: 62.0116
Evaluate side-chains
  367 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 324
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  285 PHE
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  449 SER
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  285 PHE
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  285 PHE
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  484 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 128 optimal weight:    8.9990
   chunk 135 optimal weight:   30.0000
   chunk 169 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 154 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 161 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 164 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.110462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.082288 restraints weight = 38578.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.085305 restraints weight = 24977.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.087633 restraints weight = 18129.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.089350 restraints weight = 14148.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.090652 restraints weight = 11629.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  14908  Z= 0.165
  Angle     :  0.749   9.631  20204  Z= 0.374
  Chirality :  0.047   0.220   2172
  Planarity :  0.004   0.044   2676
  Dihedral  :  5.889  60.043   2052
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 23.56 %
    Favored  : 73.43 %
  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: -0.93 (0.20), residues: 1824
  helix:  0.20 (0.17), residues: 916
  sheet: -2.90 (0.32), residues: 168
  loop : -0.94 (0.24), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 445 
 TYR   0.018   0.002   TYR D 370 
 PHE   0.011   0.002   PHE D 376 
 TRP   0.019   0.003   TRP D 371 
 HIS   0.017   0.002   HIS C 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (14904)
  covalent geometry    : angle       0.74855 (20204)
  hydrogen bonds       : bond        0.03864 (  713)
  hydrogen bonds       : angle       5.43773 ( 2079)
  Misc. bond           : bond        0.00097 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 317
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7191 (t0)
REVERT: D  273 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8531 (mm-30)
REVERT: D  282 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8954 (ptm-80)
REVERT: D  321 MET cc_start: 0.8996 (pmm) cc_final: 0.8679 (pmm)
REVERT: D  338 MET cc_start: 0.9260 (mmm) cc_final: 0.9054 (mmt)
REVERT: D  344 PHE cc_start: 0.9631 (t80) cc_final: 0.9399 (t80)
REVERT: D  356 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8736 (mm)
REVERT: D  441 LYS cc_start: 0.9624 (tmtt) cc_final: 0.9178 (tptp)
REVERT: D  445 ARG cc_start: 0.9416 (tpp80) cc_final: 0.9177 (tpp80)
REVERT: A  174 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7152 (t0)
REVERT: A  321 MET cc_start: 0.9006 (pmm) cc_final: 0.8702 (pmm)
REVERT: A  356 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8734 (mm)
REVERT: A  441 LYS cc_start: 0.9637 (tmtt) cc_final: 0.9191 (tptp)
REVERT: B  174 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7155 (t0)
REVERT: B  273 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8524 (mm-30)
REVERT: B  282 ARG cc_start: 0.9181 (ttm-80) cc_final: 0.8941 (ptm-80)
REVERT: B  321 MET cc_start: 0.8996 (pmm) cc_final: 0.8694 (pmm)
REVERT: B  338 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8454 (tpt)
REVERT: B  344 PHE cc_start: 0.9638 (t80) cc_final: 0.9319 (t80)
REVERT: B  356 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8707 (mm)
REVERT: B  441 LYS cc_start: 0.9581 (tmtt) cc_final: 0.9176 (tptp)
REVERT: C  174 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7142 (t0)
REVERT: C  321 MET cc_start: 0.8994 (pmm) cc_final: 0.8692 (pmm)
REVERT: C  338 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8465 (tpt)
REVERT: C  344 PHE cc_start: 0.9632 (t80) cc_final: 0.9314 (t80)
REVERT: C  356 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8700 (mm)
REVERT: C  441 LYS cc_start: 0.9640 (tmtt) cc_final: 0.9196 (tptp)
  outliers start: 46
  outliers final: 32
  residues processed: 344
  average time/residue: 0.0999
  time to fit residues: 53.0442
Evaluate side-chains
  346 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 304
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  393 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  449 SER
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  338 MET
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 MET
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  484 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 148 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 116 optimal weight:    0.8980
   chunk 95 optimal weight:    0.0170
   chunk 48 optimal weight:    9.9990
   chunk 178 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 63 optimal weight:    7.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.9020

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

Flipped N/Q/H residues before XYZ refinement:
D 271 GLN
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 483 GLN
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 GLN
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 483 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.112684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.083827 restraints weight = 37022.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.086906 restraints weight = 24160.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.089246 restraints weight = 17608.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.091086 restraints weight = 13817.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.092440 restraints weight = 11391.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14908  Z= 0.132
  Angle     :  0.766  11.403  20204  Z= 0.376
  Chirality :  0.046   0.174   2172
  Planarity :  0.005   0.042   2676
  Dihedral  :  5.894  62.387   2052
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 25.00 %
    Favored  : 72.26 %
  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: -0.88 (0.20), residues: 1824
  helix:  0.20 (0.17), residues: 912
  sheet: -2.80 (0.33), residues: 168
  loop : -0.89 (0.24), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 203 
 TYR   0.015   0.001   TYR B 313 
 PHE   0.023   0.002   PHE B 285 
 TRP   0.019   0.003   TRP D 232 
 HIS   0.010   0.002   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (14904)
  covalent geometry    : angle       0.76650 (20204)
  hydrogen bonds       : bond        0.03706 (  713)
  hydrogen bonds       : angle       5.36351 ( 2079)
  Misc. bond           : bond        0.00083 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 338
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  174 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7043 (t0)
REVERT: D  273 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8486 (mm-30)
REVERT: D  282 ARG cc_start: 0.9205 (ttm-80) cc_final: 0.8644 (mtp-110)
REVERT: D  321 MET cc_start: 0.8967 (pmm) cc_final: 0.8667 (pmm)
REVERT: D  338 MET cc_start: 0.9278 (mmm) cc_final: 0.8965 (mmt)
REVERT: D  356 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8787 (mm)
REVERT: D  441 LYS cc_start: 0.9587 (tmtt) cc_final: 0.8946 (tptp)
REVERT: D  443 LYS cc_start: 0.9497 (tttt) cc_final: 0.9154 (ptmt)
REVERT: D  445 ARG cc_start: 0.9466 (tpp80) cc_final: 0.8825 (tpp-160)
REVERT: A  174 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7023 (t0)
REVERT: A  273 GLU cc_start: 0.8791 (mm-30) cc_final: 0.7272 (pp20)
REVERT: A  356 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8777 (mm)
REVERT: A  441 LYS cc_start: 0.9607 (tmtt) cc_final: 0.9191 (tptp)
REVERT: A  443 LYS cc_start: 0.9451 (tttt) cc_final: 0.9113 (ptmt)
REVERT: B  174 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6992 (t0)
REVERT: B  273 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8506 (mm-30)
REVERT: B  356 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8786 (mm)
REVERT: B  441 LYS cc_start: 0.9611 (tmtt) cc_final: 0.8761 (tptp)
REVERT: B  443 LYS cc_start: 0.9474 (tttt) cc_final: 0.9151 (ptmt)
REVERT: B  445 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8705 (tpp-160)
REVERT: C  174 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7017 (t0)
REVERT: C  273 GLU cc_start: 0.8785 (mm-30) cc_final: 0.7271 (pp20)
REVERT: C  282 ARG cc_start: 0.9221 (ttm-80) cc_final: 0.8653 (tmm-80)
REVERT: C  344 PHE cc_start: 0.9666 (t80) cc_final: 0.9446 (t80)
REVERT: C  356 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8777 (mm)
REVERT: C  441 LYS cc_start: 0.9609 (tmtt) cc_final: 0.9194 (tptp)
REVERT: C  443 LYS cc_start: 0.9449 (tttt) cc_final: 0.9111 (ptmt)
  outliers start: 42
  outliers final: 29
  residues processed: 359
  average time/residue: 0.1094
  time to fit residues: 58.8907
Evaluate side-chains
  349 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 312
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 ASP
Chi-restraints excluded: chain D residue  246 HIS
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  332 LEU
Chi-restraints excluded: chain D residue  356 LEU
Chi-restraints excluded: chain D residue  430 VAL
Chi-restraints excluded: chain D residue  444 LEU
Chi-restraints excluded: chain D residue  449 SER
Chi-restraints excluded: chain D residue  484 ASP
Chi-restraints excluded: chain A residue  174 ASP
Chi-restraints excluded: chain A residue  246 HIS
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  246 HIS
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  444 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain C residue  113 LEU
Chi-restraints excluded: chain C residue  174 ASP
Chi-restraints excluded: chain C residue  246 HIS
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain C residue  430 VAL
Chi-restraints excluded: chain C residue  444 LEU
Chi-restraints excluded: chain C residue  449 SER
Chi-restraints excluded: chain C residue  484 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 85 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 120 optimal weight:    0.9980
   chunk 133 optimal weight:    0.0770
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 134 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   chunk 163 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    3.6144

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

Flipped N/Q/H residues before XYZ refinement:
** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 HIS
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** 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 = 0.3749 r_free = 0.3749 target = 0.109996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.082108 restraints weight = 38722.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.085115 restraints weight = 25121.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.087412 restraints weight = 18248.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.089090 restraints weight = 14214.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.090442 restraints weight = 11703.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.5696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14908  Z= 0.199
  Angle     :  0.776  10.827  20204  Z= 0.392
  Chirality :  0.048   0.233   2172
  Planarity :  0.005   0.040   2676
  Dihedral  :  5.863  57.673   2052
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 21.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 25.39 %
    Favored  : 72.00 %
  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: -0.98 (0.20), residues: 1824
  helix:  0.11 (0.17), residues: 912
  sheet: -3.06 (0.30), residues: 168
  loop : -0.87 (0.24), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 445 
 TYR   0.027   0.002   TYR D 213 
 PHE   0.027   0.002   PHE D 285 
 TRP   0.022   0.003   TRP A 371 
 HIS   0.015   0.002   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (14904)
  covalent geometry    : angle       0.77627 (20204)
  hydrogen bonds       : bond        0.03840 (  713)
  hydrogen bonds       : angle       5.48757 ( 2079)
  Misc. bond           : bond        0.00097 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2284.80 seconds
wall clock time: 40 minutes 15.41 seconds (2415.41 seconds total)