Starting phenix.real_space_refine
on Tue Jan 21 06:28:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wzk_37955/01_2025/8wzk_37955.cif"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      12      5.49       5
     S      52      5.16       5
     C   10392      2.51       5
     N    2884      2.21       5
     O    3024      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 16368
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4001
          Classifications: {'peptide': 497}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460}
    Chain: "A"
      Number of atoms: 91
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 91
          Unusual residues: {'HEM': 1, 'NDP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 8.31, per 1000 atoms: 0.51
  Number of scatterers: 16368
  At special positions: 0
  Unit cell: (108.07, 114.49, 84.53, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      52     16.00
     P      12     15.00
     O    3024      8.00
     N    2884      7.00
     C   10392      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: 4.43
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3712

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 8 sheets defined
      39.0% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.91
  Creating SS restraints...
    Processing helix  chain 'B' and resid 10 through 19
    Processing helix  chain 'B' and resid 54 through 65
    Processing helix  chain 'B' and resid 97 through 101
    Processing helix  chain 'B' and resid 157 through 159
      No H-bonds generated for 'chain 'B' and resid 157 through 159'
    Processing helix  chain 'B' and resid 160 through 169
    Processing helix  chain 'B' and resid 178 through 189
    Processing helix  chain 'B' and resid 192 through 201
    Processing helix  chain 'B' and resid 202 through 205
      removed outlier: 3.625A  pdb=" N   ILE B 205 " --> pdb=" O   ASP B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 205'
    Processing helix  chain 'B' and resid 246 through 257
      removed outlier: 3.895A  pdb=" N   GLN B 255 " --> pdb=" O   ALA B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 272
    Processing helix  chain 'B' and resid 285 through 291
    Processing helix  chain 'B' and resid 324 through 329
    Processing helix  chain 'B' and resid 348 through 366
      removed outlier: 3.912A  pdb=" N   PHE B 356 " --> pdb=" O   GLN B 352 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR B 358 " --> pdb=" O   ARG B 354 " (cutoff:3.500A)
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 369 through 373
    Processing helix  chain 'B' and resid 415 through 419
      removed outlier: 3.642A  pdb=" N   LEU B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 450
    Processing helix  chain 'B' and resid 452 through 468
    Processing helix  chain 'B' and resid 471 through 486
    Processing helix  chain 'B' and resid 486 through 501
    Processing helix  chain 'A' and resid 10 through 19
    Processing helix  chain 'A' and resid 54 through 65
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 157 through 159
      No H-bonds generated for 'chain 'A' and resid 157 through 159'
    Processing helix  chain 'A' and resid 160 through 169
    Processing helix  chain 'A' and resid 178 through 189
    Processing helix  chain 'A' and resid 192 through 201
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 3.625A  pdb=" N   ILE A 205 " --> pdb=" O   ASP A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 246 through 257
      removed outlier: 3.895A  pdb=" N   GLN A 255 " --> pdb=" O   ALA A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 272
    Processing helix  chain 'A' and resid 285 through 291
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 348 through 366
      removed outlier: 3.912A  pdb=" N   PHE A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A 358 " --> pdb=" O   ARG A 354 " (cutoff:3.500A)
      Proline residue:  A 359  - end of helix
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 415 through 419
      removed outlier: 3.642A  pdb=" N   LEU A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 450
    Processing helix  chain 'A' and resid 452 through 468
    Processing helix  chain 'A' and resid 471 through 486
    Processing helix  chain 'A' and resid 486 through 501
    Processing helix  chain 'C' and resid 10 through 19
    Processing helix  chain 'C' and resid 54 through 65
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 157 through 159
      No H-bonds generated for 'chain 'C' and resid 157 through 159'
    Processing helix  chain 'C' and resid 160 through 169
    Processing helix  chain 'C' and resid 178 through 189
    Processing helix  chain 'C' and resid 192 through 201
    Processing helix  chain 'C' and resid 202 through 205
      removed outlier: 3.625A  pdb=" N   ILE C 205 " --> pdb=" O   ASP C 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 202 through 205'
    Processing helix  chain 'C' and resid 246 through 257
      removed outlier: 3.895A  pdb=" N   GLN C 255 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 259 through 272
    Processing helix  chain 'C' and resid 285 through 291
    Processing helix  chain 'C' and resid 324 through 329
    Processing helix  chain 'C' and resid 348 through 366
      removed outlier: 3.912A  pdb=" N   PHE C 356 " --> pdb=" O   GLN C 352 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR C 358 " --> pdb=" O   ARG C 354 " (cutoff:3.500A)
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 369 through 373
    Processing helix  chain 'C' and resid 415 through 419
      removed outlier: 3.641A  pdb=" N   LEU C 419 " --> pdb=" O   PRO C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 440 through 450
    Processing helix  chain 'C' and resid 452 through 468
    Processing helix  chain 'C' and resid 471 through 486
    Processing helix  chain 'C' and resid 486 through 501
    Processing helix  chain 'D' and resid 10 through 19
    Processing helix  chain 'D' and resid 54 through 65
    Processing helix  chain 'D' and resid 97 through 101
    Processing helix  chain 'D' and resid 157 through 159
      No H-bonds generated for 'chain 'D' and resid 157 through 159'
    Processing helix  chain 'D' and resid 160 through 169
    Processing helix  chain 'D' and resid 178 through 189
    Processing helix  chain 'D' and resid 192 through 201
    Processing helix  chain 'D' and resid 202 through 205
      removed outlier: 3.625A  pdb=" N   ILE D 205 " --> pdb=" O   ASP D 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 202 through 205'
    Processing helix  chain 'D' and resid 246 through 257
      removed outlier: 3.895A  pdb=" N   GLN D 255 " --> pdb=" O   ALA D 251 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 272
    Processing helix  chain 'D' and resid 285 through 291
    Processing helix  chain 'D' and resid 324 through 329
    Processing helix  chain 'D' and resid 348 through 366
      removed outlier: 3.912A  pdb=" N   PHE D 356 " --> pdb=" O   GLN D 352 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR D 358 " --> pdb=" O   ARG D 354 " (cutoff:3.500A)
      Proline residue:  D 359  - end of helix
    Processing helix  chain 'D' and resid 369 through 373
    Processing helix  chain 'D' and resid 415 through 419
      removed outlier: 3.642A  pdb=" N   LEU D 419 " --> pdb=" O   PRO D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 440 through 450
    Processing helix  chain 'D' and resid 452 through 468
    Processing helix  chain 'D' and resid 471 through 486
    Processing helix  chain 'D' and resid 486 through 501
    Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44
      removed outlier: 3.979A  pdb=" N   ILE A 423 " --> pdb=" O   VAL D 429 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 345
      removed outlier: 5.955A  pdb=" N   ILE B 281 " --> pdb=" O   PRO B 312 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   LEU B 316 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   GLU B  86 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU B 318 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR B  84 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 423 through 424
      removed outlier: 3.979A  pdb=" N   ILE B 423 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 423 through 424
      removed outlier: 3.979A  pdb=" N   ILE C 423 " --> pdb=" O   VAL B 429 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345
      removed outlier: 5.954A  pdb=" N   ILE A 281 " --> pdb=" O   PRO A 312 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   LEU A 316 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   GLU A  86 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU A 318 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR A  84 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 44
      removed outlier: 3.977A  pdb=" N   ILE D 423 " --> pdb=" O   VAL A 429 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345
      removed outlier: 5.955A  pdb=" N   ILE C 281 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   LEU C 316 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   GLU C  86 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   LEU C 318 " --> pdb=" O   TYR C  84 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR C  84 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345
      removed outlier: 5.954A  pdb=" N   ILE D 281 " --> pdb=" O   PRO D 312 " (cutoff:3.500A)
      removed outlier: 5.668A  pdb=" N   LEU D 316 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   GLU D  86 " --> pdb=" O   LEU D 316 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   LEU D 318 " --> pdb=" O   TYR D  84 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   TYR D  84 " --> pdb=" O   LEU D 318 " (cutoff:3.500A)

    660 hydrogen bonds defined for protein.
    1884 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: 5.64

  Time building geometry restraints manager: 4.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.37: 5884
        1.37 -     1.56: 10880
        1.56 -     1.76: 20
        1.76 -     1.95: 92
        1.95 -     2.14: 12
  Bond restraints: 16888
  Sorted by residual:
  bond pdb=" O2B NDP D3002 "
       pdb=" P2B NDP D3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.620  0.213 3.80e-02 6.93e+02 3.13e+01
  bond pdb=" O2B NDP A3002 "
       pdb=" P2B NDP A3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.620  0.213 3.80e-02 6.93e+02 3.13e+01
  bond pdb=" O2B NDP C3002 "
       pdb=" P2B NDP C3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.620  0.213 3.80e-02 6.93e+02 3.13e+01
  bond pdb=" O2B NDP B3002 "
       pdb=" P2B NDP B3002 "
    ideal  model  delta    sigma   weight residual
    1.833  1.621  0.212 3.80e-02 6.93e+02 3.11e+01
  bond pdb=" C   VAL D 111 "
       pdb=" O   VAL D 111 "
    ideal  model  delta    sigma   weight residual
    1.236  1.283 -0.047 1.02e-02 9.61e+03 2.10e+01
  ... (remaining 16883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.45: 22690
        4.45 -     8.89: 318
        8.89 -    13.34: 20
       13.34 -    17.79: 8
       17.79 -    22.23: 4
  Bond angle restraints: 23040
  Sorted by residual:
  angle pdb=" PA  NDP B3002 "
        pdb=" O3  NDP B3002 "
        pdb=" PN  NDP B3002 "
      ideal   model   delta    sigma   weight residual
     107.74  129.97  -22.23 1.95e+00 2.62e-01 1.29e+02
  angle pdb=" PA  NDP D3002 "
        pdb=" O3  NDP D3002 "
        pdb=" PN  NDP D3002 "
      ideal   model   delta    sigma   weight residual
     107.74  129.97  -22.23 1.95e+00 2.62e-01 1.29e+02
  angle pdb=" PA  NDP C3002 "
        pdb=" O3  NDP C3002 "
        pdb=" PN  NDP C3002 "
      ideal   model   delta    sigma   weight residual
     107.74  129.96  -22.22 1.95e+00 2.62e-01 1.29e+02
  angle pdb=" PA  NDP A3002 "
        pdb=" O3  NDP A3002 "
        pdb=" PN  NDP A3002 "
      ideal   model   delta    sigma   weight residual
     107.74  129.96  -22.22 1.95e+00 2.62e-01 1.29e+02
  angle pdb=" C5B NDP B3002 "
        pdb=" O5B NDP B3002 "
        pdb=" PA  NDP B3002 "
      ideal   model   delta    sigma   weight residual
     103.84  121.48  -17.64 1.91e+00 2.73e-01 8.48e+01
  ... (remaining 23035 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.79: 9102
       19.79 -    39.59: 589
       39.59 -    59.38: 113
       59.38 -    79.17: 40
       79.17 -    98.96: 16
  Dihedral angle restraints: 9860
    sinusoidal: 4080
      harmonic: 5780
  Sorted by residual:
  dihedral pdb=" CA  ASP A 389 "
           pdb=" C   ASP A 389 "
           pdb=" N   GLY A 390 "
           pdb=" CA  GLY A 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.53   25.47     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASP C 389 "
           pdb=" C   ASP C 389 "
           pdb=" N   GLY C 390 "
           pdb=" CA  GLY C 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ASP B 389 "
           pdb=" C   ASP B 389 "
           pdb=" N   GLY B 390 "
           pdb=" CA  GLY B 390 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 9857 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 971
       0.048 -    0.096: 759
       0.096 -    0.144: 443
       0.144 -    0.192: 120
       0.192 -    0.241: 35
  Chirality restraints: 2328
  Sorted by residual:
  chirality pdb=" CA  ILE B 311 "
            pdb=" N   ILE B 311 "
            pdb=" C   ILE B 311 "
            pdb=" CB  ILE B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CA  ILE D 311 "
            pdb=" N   ILE D 311 "
            pdb=" C   ILE D 311 "
            pdb=" CB  ILE D 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  ILE A 311 "
            pdb=" N   ILE A 311 "
            pdb=" C   ILE A 311 "
            pdb=" CB  ILE A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 2325 not shown)

  Planarity restraints: 3052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEM D3001 "    0.072 2.00e-02 2.50e+03   4.02e-02 3.63e+01
        pdb=" C2C HEM D3001 "    0.049 2.00e-02 2.50e+03
        pdb=" C3C HEM D3001 "    0.006 2.00e-02 2.50e+03
        pdb=" C4C HEM D3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAC HEM D3001 "   -0.040 2.00e-02 2.50e+03
        pdb=" CHC HEM D3001 "   -0.071 2.00e-02 2.50e+03
        pdb=" CHD HEM D3001 "    0.005 2.00e-02 2.50e+03
        pdb=" CMC HEM D3001 "   -0.004 2.00e-02 2.50e+03
        pdb=" NC  HEM D3001 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEM B3001 "    0.072 2.00e-02 2.50e+03   4.00e-02 3.59e+01
        pdb=" C2C HEM B3001 "    0.049 2.00e-02 2.50e+03
        pdb=" C3C HEM B3001 "    0.007 2.00e-02 2.50e+03
        pdb=" C4C HEM B3001 "   -0.014 2.00e-02 2.50e+03
        pdb=" CAC HEM B3001 "   -0.040 2.00e-02 2.50e+03
        pdb=" CHC HEM B3001 "   -0.070 2.00e-02 2.50e+03
        pdb=" CHD HEM B3001 "    0.005 2.00e-02 2.50e+03
        pdb=" CMC HEM B3001 "   -0.004 2.00e-02 2.50e+03
        pdb=" NC  HEM B3001 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEM C3001 "   -0.072 2.00e-02 2.50e+03   3.99e-02 3.58e+01
        pdb=" C2C HEM C3001 "   -0.049 2.00e-02 2.50e+03
        pdb=" C3C HEM C3001 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4C HEM C3001 "    0.014 2.00e-02 2.50e+03
        pdb=" CAC HEM C3001 "    0.039 2.00e-02 2.50e+03
        pdb=" CHC HEM C3001 "    0.070 2.00e-02 2.50e+03
        pdb=" CHD HEM C3001 "   -0.005 2.00e-02 2.50e+03
        pdb=" CMC HEM C3001 "    0.004 2.00e-02 2.50e+03
        pdb=" NC  HEM C3001 "    0.005 2.00e-02 2.50e+03
  ... (remaining 3049 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 5403
        2.88 -     3.39: 15743
        3.39 -     3.89: 30676
        3.89 -     4.40: 35266
        4.40 -     4.90: 57765
  Nonbonded interactions: 144853
  Sorted by model distance:
  nonbonded pdb=" O   ARG D 388 "
            pdb=" O   ASP D 389 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" O   ARG A 388 "
            pdb=" O   ASP A 389 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" O   ARG B 388 "
            pdb=" O   ASP B 389 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" O   ARG C 388 "
            pdb=" O   ASP C 389 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" OD1 ASP A 298 "
            pdb=" OG1 THR A 300 "
     model   vdw
     2.389 3.040
  ... (remaining 144848 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  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:             0.020
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     35.790
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:11.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
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      :  0.016   0.213  16888  Z= 1.035
  Angle     :  1.797  22.233  23040  Z= 1.232
  Chirality :  0.082   0.241   2328
  Planarity :  0.009   0.045   3052
  Dihedral  : 14.605  98.964   6148
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.84 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  4.67 %
    Favored  : 93.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.17), residues: 1980
  helix: -0.51 (0.17), residues: 684
  sheet: -0.29 (0.31), residues: 276
  loop : -1.06 (0.18), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.012   TRP C 277 
 HIS   0.031   0.006   HIS B 218 
 PHE   0.046   0.009   PHE B 334 
 TYR   0.038   0.009   TYR A 236 
 ARG   0.034   0.003   ARG C  72 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 332
  time to evaluate  : 1.879 
Fit side-chains
REVERT: B   12 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.5776 (mtm)
REVERT: B   93 LYS cc_start: 0.6283 (ptmt) cc_final: 0.5971 (mtpt)
REVERT: B   94 TYR cc_start: 0.6983 (m-80) cc_final: 0.6775 (m-80)
REVERT: B   98 LYS cc_start: 0.6813 (mttt) cc_final: 0.6305 (mtpt)
REVERT: B  139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10)
REVERT: B  140 ASP cc_start: 0.6392 (m-30) cc_final: 0.6190 (m-30)
REVERT: B  228 GLU cc_start: 0.5895 (mp0) cc_final: 0.5649 (tt0)
REVERT: B  232 CYS cc_start: 0.7278 (t) cc_final: 0.6705 (p)
REVERT: B  256 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6185 (mt-10)
REVERT: B  273 LYS cc_start: 0.5473 (mtmm) cc_final: 0.5262 (mmtm)
REVERT: B  306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt)
REVERT: B  389 ASP cc_start: 0.5162 (OUTLIER) cc_final: 0.4598 (m-30)
REVERT: B  396 ASP cc_start: 0.5060 (p0) cc_final: 0.4731 (p0)
REVERT: B  422 SER cc_start: 0.6995 (p) cc_final: 0.6763 (t)
REVERT: B  423 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5850 (mp)
REVERT: B  428 GLU cc_start: 0.6026 (mp0) cc_final: 0.5818 (mt-10)
REVERT: B  453 GLU cc_start: 0.5781 (tp30) cc_final: 0.5378 (tp30)
REVERT: B  466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6832 (t-90)
REVERT: B  484 GLU cc_start: 0.6868 (tt0) cc_final: 0.6454 (tt0)
REVERT: A   12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5767 (mtm)
REVERT: A   93 LYS cc_start: 0.6289 (ptmt) cc_final: 0.5978 (mtpt)
REVERT: A   94 TYR cc_start: 0.6984 (m-80) cc_final: 0.6781 (m-80)
REVERT: A   98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6313 (mtpt)
REVERT: A  139 GLU cc_start: 0.5948 (mm-30) cc_final: 0.5400 (mt-10)
REVERT: A  140 ASP cc_start: 0.6395 (m-30) cc_final: 0.6192 (m-30)
REVERT: A  228 GLU cc_start: 0.5927 (mp0) cc_final: 0.5683 (tt0)
REVERT: A  232 CYS cc_start: 0.7280 (t) cc_final: 0.6703 (p)
REVERT: A  256 GLU cc_start: 0.6416 (mm-30) cc_final: 0.6197 (mt-10)
REVERT: A  273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5264 (mmtm)
REVERT: A  306 LYS cc_start: 0.6350 (mppt) cc_final: 0.6143 (mppt)
REVERT: A  389 ASP cc_start: 0.5158 (OUTLIER) cc_final: 0.4596 (m-30)
REVERT: A  396 ASP cc_start: 0.5055 (p0) cc_final: 0.4727 (p0)
REVERT: A  422 SER cc_start: 0.6994 (p) cc_final: 0.6755 (t)
REVERT: A  423 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5732 (mp)
REVERT: A  428 GLU cc_start: 0.6028 (mp0) cc_final: 0.5818 (mt-10)
REVERT: A  453 GLU cc_start: 0.5777 (tp30) cc_final: 0.5374 (tp30)
REVERT: A  466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6832 (t-90)
REVERT: A  484 GLU cc_start: 0.6884 (tt0) cc_final: 0.6468 (tt0)
REVERT: C   12 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5763 (mtm)
REVERT: C   93 LYS cc_start: 0.6282 (ptmt) cc_final: 0.5971 (mtpt)
REVERT: C   94 TYR cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80)
REVERT: C   98 LYS cc_start: 0.6818 (mttt) cc_final: 0.6477 (mttm)
REVERT: C  139 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5420 (mt-10)
REVERT: C  228 GLU cc_start: 0.5926 (mp0) cc_final: 0.5684 (tt0)
REVERT: C  232 CYS cc_start: 0.7279 (t) cc_final: 0.6703 (p)
REVERT: C  256 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6187 (mt-10)
REVERT: C  273 LYS cc_start: 0.5474 (mtmm) cc_final: 0.5262 (mmtm)
REVERT: C  306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6142 (mppt)
REVERT: C  389 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4598 (m-30)
REVERT: C  396 ASP cc_start: 0.5057 (p0) cc_final: 0.4729 (p0)
REVERT: C  422 SER cc_start: 0.6998 (p) cc_final: 0.6762 (t)
REVERT: C  423 ILE cc_start: 0.6164 (OUTLIER) cc_final: 0.5733 (mp)
REVERT: C  428 GLU cc_start: 0.6025 (mp0) cc_final: 0.5801 (mt-10)
REVERT: C  453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30)
REVERT: C  466 HIS cc_start: 0.7133 (t-90) cc_final: 0.6834 (t-90)
REVERT: C  484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0)
REVERT: D   12 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5771 (mtm)
REVERT: D   93 LYS cc_start: 0.6280 (ptmt) cc_final: 0.5970 (mtpt)
REVERT: D   94 TYR cc_start: 0.6980 (m-80) cc_final: 0.6774 (m-80)
REVERT: D   98 LYS cc_start: 0.6816 (mttt) cc_final: 0.6475 (mttm)
REVERT: D  139 GLU cc_start: 0.5952 (mm-30) cc_final: 0.5423 (mt-10)
REVERT: D  228 GLU cc_start: 0.5928 (mp0) cc_final: 0.5685 (tt0)
REVERT: D  232 CYS cc_start: 0.7279 (t) cc_final: 0.6704 (p)
REVERT: D  256 GLU cc_start: 0.6406 (mm-30) cc_final: 0.6193 (mt-10)
REVERT: D  273 LYS cc_start: 0.5475 (mtmm) cc_final: 0.5263 (mmtm)
REVERT: D  306 LYS cc_start: 0.6351 (mppt) cc_final: 0.6143 (mppt)
REVERT: D  389 ASP cc_start: 0.5163 (OUTLIER) cc_final: 0.4599 (m-30)
REVERT: D  396 ASP cc_start: 0.5058 (p0) cc_final: 0.4701 (p0)
REVERT: D  422 SER cc_start: 0.6998 (p) cc_final: 0.6761 (t)
REVERT: D  423 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5734 (mp)
REVERT: D  428 GLU cc_start: 0.6027 (mp0) cc_final: 0.5816 (mt-10)
REVERT: D  453 GLU cc_start: 0.5778 (tp30) cc_final: 0.5376 (tp30)
REVERT: D  466 HIS cc_start: 0.7134 (t-90) cc_final: 0.6833 (t-90)
REVERT: D  484 GLU cc_start: 0.6867 (tt0) cc_final: 0.6454 (tt0)
  outliers start: 32
  outliers final: 8
  residues processed: 348
  average time/residue: 1.3797
  time to fit residues: 531.2148
Evaluate side-chains
  264 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 244
  time to evaluate  : 1.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   12 MET
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  368 PRO
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  423 ILE
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  368 PRO
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  368 PRO
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain C residue  423 ILE
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  368 PRO
Chi-restraints excluded: chain D residue  389 ASP
Chi-restraints excluded: chain D residue  423 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    0.9990
   chunk 148 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 100 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 153 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9990
   chunk 177 optimal weight:    8.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 ASN
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 407 ASN
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 ASN
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 407 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.167861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.147250 restraints weight = 16107.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.02
r_work: 0.3518 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16888  Z= 0.176
  Angle     :  0.584   6.424  23040  Z= 0.295
  Chirality :  0.044   0.145   2328
  Planarity :  0.004   0.040   3052
  Dihedral  :  8.863 107.183   2300
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.11 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.19), residues: 1980
  helix:  1.29 (0.20), residues: 688
  sheet:  0.66 (0.31), residues: 300
  loop : -0.43 (0.19), residues: 992

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  15 
 HIS   0.003   0.001   HIS C 466 
 PHE   0.012   0.002   PHE D  57 
 TYR   0.019   0.001   TYR D 236 
 ARG   0.003   0.000   ARG C 363 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 275
  time to evaluate  : 1.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 MET cc_start: 0.7258 (mtm) cc_final: 0.6783 (mtm)
REVERT: B   93 LYS cc_start: 0.6704 (ptmt) cc_final: 0.6424 (mtmt)
REVERT: B   98 LYS cc_start: 0.7830 (mttt) cc_final: 0.7521 (mttm)
REVERT: B  139 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6183 (mm-30)
REVERT: B  180 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7286 (m-30)
REVERT: B  389 ASP cc_start: 0.5790 (OUTLIER) cc_final: 0.5113 (m-30)
REVERT: B  396 ASP cc_start: 0.6402 (p0) cc_final: 0.5867 (p0)
REVERT: B  423 ILE cc_start: 0.7650 (mm) cc_final: 0.7440 (mp)
REVERT: B  453 GLU cc_start: 0.6786 (tp30) cc_final: 0.6538 (tp30)
REVERT: A   12 MET cc_start: 0.7223 (mtm) cc_final: 0.6747 (mtm)
REVERT: A   93 LYS cc_start: 0.6704 (ptmt) cc_final: 0.6417 (mtmt)
REVERT: A   98 LYS cc_start: 0.7835 (mttt) cc_final: 0.7526 (mttm)
REVERT: A  139 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6183 (mm-30)
REVERT: A  180 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7280 (m-30)
REVERT: A  389 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5124 (m-30)
REVERT: A  396 ASP cc_start: 0.6386 (p0) cc_final: 0.5853 (p0)
REVERT: A  423 ILE cc_start: 0.7653 (mm) cc_final: 0.7440 (mp)
REVERT: A  453 GLU cc_start: 0.6811 (tp30) cc_final: 0.6563 (tp30)
REVERT: C   12 MET cc_start: 0.7240 (mtm) cc_final: 0.6758 (mtm)
REVERT: C   93 LYS cc_start: 0.6702 (ptmt) cc_final: 0.6420 (mtmt)
REVERT: C   98 LYS cc_start: 0.7747 (mttt) cc_final: 0.7198 (mtpp)
REVERT: C  139 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6179 (mm-30)
REVERT: C  180 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7309 (m-30)
REVERT: C  389 ASP cc_start: 0.5813 (OUTLIER) cc_final: 0.5133 (m-30)
REVERT: C  396 ASP cc_start: 0.6397 (p0) cc_final: 0.5862 (p0)
REVERT: C  423 ILE cc_start: 0.7657 (mm) cc_final: 0.7425 (mp)
REVERT: C  453 GLU cc_start: 0.6768 (tp30) cc_final: 0.6519 (tp30)
REVERT: D   12 MET cc_start: 0.7236 (mtm) cc_final: 0.6762 (mtm)
REVERT: D   93 LYS cc_start: 0.6703 (ptmt) cc_final: 0.6422 (mtmt)
REVERT: D   98 LYS cc_start: 0.7745 (mttt) cc_final: 0.7192 (mtpt)
REVERT: D  139 GLU cc_start: 0.6494 (mm-30) cc_final: 0.6202 (mm-30)
REVERT: D  180 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7300 (m-30)
REVERT: D  389 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5123 (m-30)
REVERT: D  396 ASP cc_start: 0.6390 (p0) cc_final: 0.5852 (p0)
REVERT: D  423 ILE cc_start: 0.7650 (mm) cc_final: 0.7412 (mp)
REVERT: D  453 GLU cc_start: 0.6771 (tp30) cc_final: 0.6522 (tp30)
  outliers start: 20
  outliers final: 8
  residues processed: 283
  average time/residue: 1.3157
  time to fit residues: 413.4601
Evaluate side-chains
  240 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 224
  time to evaluate  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  180 ASP
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  180 ASP
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  180 ASP
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  180 ASP
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 147 optimal weight:    5.9990
   chunk 182 optimal weight:    8.9990
   chunk 163 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 179 optimal weight:    8.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 369 ASN
B 421 HIS
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 369 ASN
A 421 HIS
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 369 ASN
C 421 HIS
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 369 ASN
D 421 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.160602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.140382 restraints weight = 16197.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 0.98
r_work: 0.3445 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  16888  Z= 0.351
  Angle     :  0.766  14.868  23040  Z= 0.372
  Chirality :  0.049   0.137   2328
  Planarity :  0.006   0.051   3052
  Dihedral  :  9.907 130.284   2268
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.28 %
    Favored  : 87.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.19), residues: 1980
  helix:  0.84 (0.20), residues: 708
  sheet:  0.81 (0.31), residues: 304
  loop : -0.63 (0.19), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  15 
 HIS   0.007   0.002   HIS C 218 
 PHE   0.022   0.003   PHE A 136 
 TYR   0.025   0.002   TYR B 236 
 ARG   0.008   0.001   ARG D 363 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 227
  time to evaluate  : 1.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   12 MET cc_start: 0.7236 (mtm) cc_final: 0.6832 (mtm)
REVERT: B  180 ASP cc_start: 0.7644 (m-30) cc_final: 0.7350 (m-30)
REVERT: B  423 ILE cc_start: 0.7722 (mm) cc_final: 0.7490 (mp)
REVERT: A   12 MET cc_start: 0.7196 (mtm) cc_final: 0.6773 (mtm)
REVERT: A  180 ASP cc_start: 0.7646 (m-30) cc_final: 0.7352 (m-30)
REVERT: A  423 ILE cc_start: 0.7724 (mm) cc_final: 0.7495 (mp)
REVERT: C   12 MET cc_start: 0.7253 (mtm) cc_final: 0.6855 (mtm)
REVERT: C  180 ASP cc_start: 0.7676 (m-30) cc_final: 0.7382 (m-30)
REVERT: C  423 ILE cc_start: 0.7692 (mm) cc_final: 0.7466 (mp)
REVERT: D   12 MET cc_start: 0.7250 (mtm) cc_final: 0.6856 (mtm)
REVERT: D  180 ASP cc_start: 0.7666 (m-30) cc_final: 0.7378 (m-30)
REVERT: D  423 ILE cc_start: 0.7687 (mm) cc_final: 0.7457 (mp)
  outliers start: 37
  outliers final: 24
  residues processed: 260
  average time/residue: 1.2681
  time to fit residues: 367.4804
Evaluate side-chains
  211 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 187
  time to evaluate  : 1.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0570
   chunk 24 optimal weight:    1.9990
   chunk 149 optimal weight:    0.4980
   chunk 49 optimal weight:    8.9990
   chunk 161 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 135 optimal weight:    7.9990
   chunk 189 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.5104

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

Flipped N/Q/H residues before XYZ refinement:
B  53 GLN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  53 GLN
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  53 GLN
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 GLN
** D 173 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 = 0.3794 r_free = 0.3794 target = 0.163200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.142968 restraints weight = 16226.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.00
r_work: 0.3479 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16888  Z= 0.211
  Angle     :  0.629   9.684  23040  Z= 0.310
  Chirality :  0.045   0.143   2328
  Planarity :  0.005   0.046   3052
  Dihedral  :  9.279 126.755   2268
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 10.81 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.19), residues: 1980
  helix:  1.35 (0.21), residues: 688
  sheet:  0.80 (0.32), residues: 296
  loop : -0.34 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 183 
 HIS   0.006   0.001   HIS B 218 
 PHE   0.016   0.002   PHE D 136 
 TYR   0.020   0.002   TYR D 236 
 ARG   0.004   0.000   ARG D 363 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 196
  time to evaluate  : 1.836 
Fit side-chains
REVERT: B   12 MET cc_start: 0.7215 (mtm) cc_final: 0.6750 (mtm)
REVERT: B  180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7393 (m-30)
REVERT: B  237 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7887 (mtpm)
REVERT: A   12 MET cc_start: 0.7203 (mtm) cc_final: 0.6734 (mtm)
REVERT: A  180 ASP cc_start: 0.7685 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  237 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (mtpm)
REVERT: C   12 MET cc_start: 0.7209 (mtm) cc_final: 0.6765 (mtm)
REVERT: C  180 ASP cc_start: 0.7669 (m-30) cc_final: 0.7384 (m-30)
REVERT: C  237 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7894 (mtpm)
REVERT: D   12 MET cc_start: 0.7217 (mtm) cc_final: 0.6757 (mtm)
REVERT: D  180 ASP cc_start: 0.7671 (m-30) cc_final: 0.7387 (m-30)
REVERT: D  237 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7890 (mtpm)
  outliers start: 48
  outliers final: 28
  residues processed: 234
  average time/residue: 1.3869
  time to fit residues: 359.9346
Evaluate side-chains
  219 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 187
  time to evaluate  : 1.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  237 LYS
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  237 LYS
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  237 LYS
Chi-restraints excluded: chain D residue  254 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 159 optimal weight:    3.9990
   chunk 186 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 127 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9980
   chunk 181 optimal weight:    0.0980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 421 HIS
B 466 HIS
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 HIS
A 466 HIS
C  33 ASN
** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 421 HIS
C 466 HIS
D  33 ASN
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 421 HIS
D 466 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.166934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.146556 restraints weight = 16441.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.06
r_work: 0.3520 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3427 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  16888  Z= 0.160
  Angle     :  0.554   6.504  23040  Z= 0.277
  Chirality :  0.043   0.138   2328
  Planarity :  0.004   0.046   3052
  Dihedral  :  8.427 116.761   2260
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 11.21 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.19), residues: 1980
  helix:  1.46 (0.21), residues: 696
  sheet:  0.84 (0.32), residues: 296
  loop : -0.19 (0.20), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 183 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.014   0.001   PHE D 136 
 TYR   0.018   0.001   TYR A 236 
 ARG   0.003   0.000   ARG A 363 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 214
  time to evaluate  : 1.901 
Fit side-chains
REVERT: B   12 MET cc_start: 0.7313 (mtm) cc_final: 0.6852 (mtm)
REVERT: B  180 ASP cc_start: 0.7653 (m-30) cc_final: 0.7368 (m-30)
REVERT: B  237 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (mmtt)
REVERT: B  255 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: B  389 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.5286 (m-30)
REVERT: A   12 MET cc_start: 0.7314 (mtm) cc_final: 0.6856 (mtm)
REVERT: A  180 ASP cc_start: 0.7652 (m-30) cc_final: 0.7379 (m-30)
REVERT: A  237 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7946 (mmtt)
REVERT: A  255 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: A  389 ASP cc_start: 0.5645 (OUTLIER) cc_final: 0.5299 (m-30)
REVERT: C   12 MET cc_start: 0.7314 (mtm) cc_final: 0.6885 (mtm)
REVERT: C  180 ASP cc_start: 0.7652 (m-30) cc_final: 0.7368 (m-30)
REVERT: C  237 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7940 (mmtt)
REVERT: C  255 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: C  389 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5362 (m-30)
REVERT: D   12 MET cc_start: 0.7302 (mtm) cc_final: 0.6846 (mtm)
REVERT: D  180 ASP cc_start: 0.7654 (m-30) cc_final: 0.7359 (m-30)
REVERT: D  237 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7941 (mmtt)
REVERT: D  255 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: D  389 ASP cc_start: 0.5638 (OUTLIER) cc_final: 0.5296 (m-30)
  outliers start: 46
  outliers final: 23
  residues processed: 252
  average time/residue: 1.3568
  time to fit residues: 378.4310
Evaluate side-chains
  222 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 191
  time to evaluate  : 1.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  237 LYS
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  237 LYS
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  237 LYS
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 138 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 123 optimal weight:    6.9990
   chunk 134 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 144 optimal weight:    9.9990
   chunk 194 optimal weight:    9.9990
   chunk 145 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 HIS
A  22 GLN
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
C  22 GLN
C 173 GLN
C 466 HIS
D  22 GLN
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 466 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.161739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.141205 restraints weight = 16291.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.04
r_work: 0.3455 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3362 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  16888  Z= 0.290
  Angle     :  0.705  13.511  23040  Z= 0.342
  Chirality :  0.046   0.139   2328
  Planarity :  0.005   0.048   3052
  Dihedral  :  9.343 125.860   2260
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 12.03 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.19), residues: 1980
  helix:  1.26 (0.21), residues: 688
  sheet:  0.70 (0.32), residues: 296
  loop : -0.38 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 183 
 HIS   0.006   0.002   HIS C 218 
 PHE   0.019   0.002   PHE A 136 
 TYR   0.023   0.002   TYR A 236 
 ARG   0.006   0.001   ARG B  19 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 182
  time to evaluate  : 1.817 
Fit side-chains
REVERT: B   12 MET cc_start: 0.7385 (mtm) cc_final: 0.6907 (mtm)
REVERT: B  180 ASP cc_start: 0.7687 (m-30) cc_final: 0.7398 (m-30)
REVERT: B  237 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (mtpm)
REVERT: B  255 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: B  273 LYS cc_start: 0.7500 (mttp) cc_final: 0.7193 (mmtm)
REVERT: B  389 ASP cc_start: 0.5769 (OUTLIER) cc_final: 0.5385 (m-30)
REVERT: A   12 MET cc_start: 0.7367 (mtm) cc_final: 0.6885 (mtm)
REVERT: A  180 ASP cc_start: 0.7677 (m-30) cc_final: 0.7381 (m-30)
REVERT: A  237 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (mtpm)
REVERT: A  255 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: A  273 LYS cc_start: 0.7495 (mttp) cc_final: 0.7194 (mmtm)
REVERT: A  389 ASP cc_start: 0.5781 (OUTLIER) cc_final: 0.5398 (m-30)
REVERT: C   12 MET cc_start: 0.7213 (mtm) cc_final: 0.6772 (mtm)
REVERT: C  180 ASP cc_start: 0.7681 (m-30) cc_final: 0.7407 (m-30)
REVERT: C  237 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8028 (mtpm)
REVERT: C  255 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7238 (tm-30)
REVERT: C  273 LYS cc_start: 0.7503 (mttp) cc_final: 0.7198 (mmtm)
REVERT: C  389 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5468 (m-30)
REVERT: D   12 MET cc_start: 0.7379 (mtm) cc_final: 0.6905 (mtm)
REVERT: D  180 ASP cc_start: 0.7672 (m-30) cc_final: 0.7381 (m-30)
REVERT: D  237 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8020 (mtpm)
REVERT: D  255 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7239 (tm-30)
REVERT: D  273 LYS cc_start: 0.7502 (mttp) cc_final: 0.7196 (mmtm)
REVERT: D  389 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.5398 (m-30)
  outliers start: 52
  outliers final: 38
  residues processed: 227
  average time/residue: 1.4328
  time to fit residues: 361.2544
Evaluate side-chains
  226 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 180
  time to evaluate  : 1.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  237 LYS
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   22 GLN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  139 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  237 LYS
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  139 GLU
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  237 LYS
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 163 optimal weight:    0.9980
   chunk 195 optimal weight:    5.9990
   chunk 145 optimal weight:    6.9990
   chunk 148 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 152 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 HIS
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
C 466 HIS
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 466 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.165177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.144703 restraints weight = 16341.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.04
r_work: 0.3499 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16888  Z= 0.176
  Angle     :  0.587   7.668  23040  Z= 0.290
  Chirality :  0.044   0.144   2328
  Planarity :  0.005   0.047   3052
  Dihedral  :  8.668 116.374   2260
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 12.44 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.19), residues: 1980
  helix:  1.33 (0.21), residues: 696
  sheet:  0.76 (0.32), residues: 296
  loop : -0.22 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 183 
 HIS   0.004   0.001   HIS C 218 
 PHE   0.014   0.001   PHE A 136 
 TYR   0.019   0.001   TYR C 236 
 ARG   0.006   0.000   ARG C  19 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 192
  time to evaluate  : 1.922 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 ASP cc_start: 0.7683 (m-30) cc_final: 0.7402 (m-30)
REVERT: B  255 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7265 (tm-30)
REVERT: B  273 LYS cc_start: 0.7484 (mttp) cc_final: 0.7210 (mtpp)
REVERT: B  389 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.5366 (m-30)
REVERT: B  453 GLU cc_start: 0.6990 (tp30) cc_final: 0.6531 (tp30)
REVERT: A   12 MET cc_start: 0.7276 (mtm) cc_final: 0.6858 (mtm)
REVERT: A  180 ASP cc_start: 0.7695 (m-30) cc_final: 0.7404 (m-30)
REVERT: A  255 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7295 (tm-30)
REVERT: A  273 LYS cc_start: 0.7482 (mttp) cc_final: 0.7210 (mtpp)
REVERT: A  389 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5377 (m-30)
REVERT: C   12 MET cc_start: 0.7314 (mtm) cc_final: 0.6908 (mtm)
REVERT: C  180 ASP cc_start: 0.7692 (m-30) cc_final: 0.7398 (m-30)
REVERT: C  255 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: C  273 LYS cc_start: 0.7483 (mttp) cc_final: 0.7212 (mtpp)
REVERT: C  389 ASP cc_start: 0.5773 (OUTLIER) cc_final: 0.5444 (m-30)
REVERT: D  180 ASP cc_start: 0.7699 (m-30) cc_final: 0.7423 (m-30)
REVERT: D  255 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: D  273 LYS cc_start: 0.7496 (mttp) cc_final: 0.7219 (mtpp)
REVERT: D  389 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.5318 (m-30)
REVERT: D  453 GLU cc_start: 0.6988 (tp30) cc_final: 0.6536 (tp30)
  outliers start: 46
  outliers final: 31
  residues processed: 228
  average time/residue: 1.3273
  time to fit residues: 336.2413
Evaluate side-chains
  225 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 190
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 126 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 148 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0020
   chunk 73 optimal weight:    6.9990
   chunk 147 optimal weight:    0.8980
   chunk 183 optimal weight:    6.9990
   overall best weight:    1.5794

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 466 HIS
A  22 GLN
** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 HIS
C  22 GLN
** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 466 HIS
D  22 GLN
** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 466 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.163495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.143248 restraints weight = 16272.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.02
r_work: 0.3483 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16888  Z= 0.218
  Angle     :  0.640  10.958  23040  Z= 0.310
  Chirality :  0.045   0.141   2328
  Planarity :  0.005   0.047   3052
  Dihedral  :  8.751 110.868   2260
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 12.73 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.19), residues: 1980
  helix:  1.34 (0.21), residues: 688
  sheet:  0.66 (0.32), residues: 296
  loop : -0.25 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 183 
 HIS   0.006   0.001   HIS C 218 
 PHE   0.016   0.002   PHE A 136 
 TYR   0.020   0.002   TYR C 236 
 ARG   0.006   0.000   ARG C  19 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 186
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 ASP cc_start: 0.7677 (m-30) cc_final: 0.7395 (m-30)
REVERT: B  255 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7295 (tm-30)
REVERT: B  273 LYS cc_start: 0.7485 (mttp) cc_final: 0.7184 (mmtm)
REVERT: B  389 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5322 (m-30)
REVERT: B  396 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6258 (p0)
REVERT: A   12 MET cc_start: 0.7297 (mtm) cc_final: 0.6855 (mtm)
REVERT: A  180 ASP cc_start: 0.7689 (m-30) cc_final: 0.7409 (m-30)
REVERT: A  255 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: A  273 LYS cc_start: 0.7469 (mttp) cc_final: 0.7181 (mmtm)
REVERT: A  389 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5350 (m-30)
REVERT: C   12 MET cc_start: 0.7372 (mtm) cc_final: 0.6949 (mtm)
REVERT: C  180 ASP cc_start: 0.7690 (m-30) cc_final: 0.7397 (m-30)
REVERT: C  255 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: C  273 LYS cc_start: 0.7465 (mttp) cc_final: 0.7185 (mmtm)
REVERT: C  389 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5350 (m-30)
REVERT: D  180 ASP cc_start: 0.7682 (m-30) cc_final: 0.7396 (m-30)
REVERT: D  255 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7289 (tm-30)
REVERT: D  273 LYS cc_start: 0.7495 (mttp) cc_final: 0.7192 (mmtm)
REVERT: D  389 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5402 (m-30)
REVERT: D  394 MET cc_start: 0.6831 (mpp) cc_final: 0.6631 (mpp)
  outliers start: 56
  outliers final: 42
  residues processed: 231
  average time/residue: 1.3468
  time to fit residues: 344.7541
Evaluate side-chains
  231 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 184
  time to evaluate  : 1.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 GLN
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain A residue   22 GLN
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   22 GLN
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 137 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 148 optimal weight:    0.2980
   chunk 159 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
B  22 GLN
B 173 GLN
B 466 HIS
A  22 GLN
A 173 GLN
A 466 HIS
C  22 GLN
C 466 HIS
D  22 GLN
D 173 GLN
D 466 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.159906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.139217 restraints weight = 16386.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.04
r_work: 0.3433 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086  16888  Z= 0.397
  Angle     :  0.829  17.343  23040  Z= 0.396
  Chirality :  0.050   0.151   2328
  Planarity :  0.006   0.050   3052
  Dihedral  :  9.517 112.387   2260
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.26 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.19), residues: 1980
  helix:  0.81 (0.20), residues: 704
  sheet:  0.57 (0.31), residues: 304
  loop : -0.68 (0.18), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 186 
 HIS   0.007   0.002   HIS C 466 
 PHE   0.023   0.003   PHE A 136 
 TYR   0.023   0.002   TYR B 236 
 ARG   0.007   0.001   ARG D 363 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 181
  time to evaluate  : 1.800 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 ASP cc_start: 0.7653 (m-30) cc_final: 0.7360 (m-30)
REVERT: B  255 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: A   12 MET cc_start: 0.7302 (mtm) cc_final: 0.6967 (mtm)
REVERT: A  180 ASP cc_start: 0.7661 (m-30) cc_final: 0.7363 (m-30)
REVERT: A  255 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: C   12 MET cc_start: 0.7302 (mtm) cc_final: 0.6846 (mtm)
REVERT: C  180 ASP cc_start: 0.7668 (m-30) cc_final: 0.7380 (m-30)
REVERT: C  255 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7342 (tm-30)
REVERT: D  180 ASP cc_start: 0.7658 (m-30) cc_final: 0.7365 (m-30)
REVERT: D  255 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7347 (tm-30)
  outliers start: 48
  outliers final: 43
  residues processed: 225
  average time/residue: 1.3992
  time to fit residues: 348.7405
Evaluate side-chains
  224 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 181
  time to evaluate  : 1.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  139 GLU
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  228 GLU
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 171 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 172 optimal weight:    6.9990
   chunk 168 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0970
   chunk 46 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 178 optimal weight:    0.0770
   overall best weight:    1.2340

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

Flipped N/Q/H residues before XYZ refinement:
B 466 HIS
A 466 HIS
C 466 HIS
D 466 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.164207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.143699 restraints weight = 16378.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.04
r_work: 0.3486 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.75 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16888  Z= 0.203
  Angle     :  0.641  10.403  23040  Z= 0.312
  Chirality :  0.044   0.142   2328
  Planarity :  0.005   0.047   3052
  Dihedral  :  8.649  99.978   2260
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.79 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.19), residues: 1980
  helix:  1.33 (0.21), residues: 684
  sheet:  0.53 (0.31), residues: 296
  loop : -0.28 (0.19), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 183 
 HIS   0.006   0.001   HIS B 466 
 PHE   0.015   0.002   PHE A 136 
 TYR   0.018   0.001   TYR A 236 
 ARG   0.005   0.000   ARG B  19 

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

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

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3960 Ramachandran restraints generated.
    1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 1.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  180 ASP cc_start: 0.7713 (m-30) cc_final: 0.7417 (m-30)
REVERT: B  255 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: B  273 LYS cc_start: 0.7443 (mttp) cc_final: 0.7183 (mmtm)
REVERT: B  290 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6178 (mp0)
REVERT: B  389 ASP cc_start: 0.5737 (OUTLIER) cc_final: 0.5383 (m-30)
REVERT: A   12 MET cc_start: 0.7266 (mtm) cc_final: 0.6861 (mtm)
REVERT: A  180 ASP cc_start: 0.7701 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  255 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: A  273 LYS cc_start: 0.7442 (mttp) cc_final: 0.7200 (mmtm)
REVERT: A  389 ASP cc_start: 0.5749 (OUTLIER) cc_final: 0.5325 (m-30)
REVERT: C   12 MET cc_start: 0.7290 (mtm) cc_final: 0.6911 (mtm)
REVERT: C  180 ASP cc_start: 0.7716 (m-30) cc_final: 0.7437 (m-30)
REVERT: C  255 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7256 (tm-30)
REVERT: C  273 LYS cc_start: 0.7439 (mttp) cc_final: 0.7185 (mmtm)
REVERT: C  389 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5422 (m-30)
REVERT: D  180 ASP cc_start: 0.7728 (m-30) cc_final: 0.7434 (m-30)
REVERT: D  255 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7257 (tm-30)
REVERT: D  273 LYS cc_start: 0.7465 (mttp) cc_final: 0.7194 (mmtm)
REVERT: D  290 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6192 (mp0)
REVERT: D  389 ASP cc_start: 0.5758 (OUTLIER) cc_final: 0.5419 (m-30)
  outliers start: 42
  outliers final: 34
  residues processed: 220
  average time/residue: 1.3379
  time to fit residues: 326.4930
Evaluate side-chains
  223 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 185
  time to evaluate  : 1.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   93 LYS
Chi-restraints excluded: chain B residue  120 SER
Chi-restraints excluded: chain B residue  128 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  236 TYR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  120 SER
Chi-restraints excluded: chain A residue  128 ASP
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   93 LYS
Chi-restraints excluded: chain C residue  120 SER
Chi-restraints excluded: chain C residue  128 ASP
Chi-restraints excluded: chain C residue  138 THR
Chi-restraints excluded: chain C residue  150 THR
Chi-restraints excluded: chain C residue  236 TYR
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  254 SER
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain D residue   51 LEU
Chi-restraints excluded: chain D residue   93 LYS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 THR
Chi-restraints excluded: chain D residue  150 THR
Chi-restraints excluded: chain D residue  236 TYR
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  254 SER
Chi-restraints excluded: chain D residue  389 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 181 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 109 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   chunk 177 optimal weight:    0.0980
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B 466 HIS
A 466 HIS
C 466 HIS
D 466 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.164941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.144413 restraints weight = 16274.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.04
r_work: 0.3494 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16888  Z= 0.199
  Angle     :  0.640  12.963  23040  Z= 0.309
  Chirality :  0.044   0.141   2328
  Planarity :  0.005   0.048   3052
  Dihedral  :  8.344  91.404   2260
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.31 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.19), residues: 1980
  helix:  1.39 (0.21), residues: 684
  sheet:  0.61 (0.32), residues: 292
  loop : -0.21 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 183 
 HIS   0.005   0.001   HIS B 466 
 PHE   0.015   0.002   PHE B 136 
 TYR   0.018   0.001   TYR D 236 
 ARG   0.004   0.000   ARG D  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12277.53 seconds
wall clock time: 217 minutes 41.01 seconds (13061.01 seconds total)