Starting phenix.real_space_refine
on Wed Mar  4 19:56:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cr4_30447/03_2026/7cr4_30447.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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
     S      88      5.16       5
     Cl      4      4.86       5
     C   10288      2.51       5
     N    2724      2.21       5
     O    2880      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15988
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2855
          Classifications: {'peptide': 349}
          Link IDs: {'PTRANS': 6, 'TRANS': 342}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 143, 1125
          Classifications: {'peptide': 143}
          Link IDs: {'PTRANS': 2, 'TRANS': 140}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'GB9': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, D, F, C, E, G
  Time building chain proxies: 2.61, per 1000 atoms: 0.16
  Number of scatterers: 15988
  At special positions: 0
  Unit cell: (126.75, 126.75, 119.652, 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)
     Cl      4     17.00
     S      88     16.00
     F       4      9.00
     O    2880      8.00
     N    2724      7.00
     C   10288      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 705.7 milliseconds
  

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3664

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 8 sheets defined
      80.5% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 86
    Processing helix  chain 'A' and resid 90 through 114
    Processing helix  chain 'A' and resid 115 through 119
      removed outlier: 3.778A  pdb=" N   TYR A 118 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 147
    Processing helix  chain 'A' and resid 148 through 151
      removed outlier: 3.505A  pdb=" N   CYS A 151 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 148 through 151'
    Processing helix  chain 'A' and resid 157 through 165
    Processing helix  chain 'A' and resid 166 through 182
    Processing helix  chain 'A' and resid 196 through 210
    Processing helix  chain 'A' and resid 215 through 228
      removed outlier: 3.595A  pdb=" N   LYS A 219 " --> pdb=" O   GLY A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 255
    Processing helix  chain 'A' and resid 263 through 276
      removed outlier: 3.568A  pdb=" N   ALA A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 329
      removed outlier: 3.892A  pdb=" N   THR A 296 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   SER A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      Proline residue:  A 308  - end of helix
    Processing helix  chain 'A' and resid 332 through 350
    Processing helix  chain 'A' and resid 357 through 366
    Processing helix  chain 'A' and resid 536 through 559
    Processing helix  chain 'A' and resid 562 through 594
    Processing helix  chain 'H' and resid 7 through 21
    Processing helix  chain 'H' and resid 29 through 41
    Processing helix  chain 'H' and resid 45 through 57
    Processing helix  chain 'H' and resid 66 through 74
    Processing helix  chain 'H' and resid 82 through 93
    Processing helix  chain 'H' and resid 103 through 111
    Processing helix  chain 'H' and resid 118 through 130
    Processing helix  chain 'H' and resid 139 through 148
    Processing helix  chain 'B' and resid 71 through 86
    Processing helix  chain 'B' and resid 90 through 114
    Processing helix  chain 'B' and resid 115 through 119
      removed outlier: 3.778A  pdb=" N   TYR B 118 " --> pdb=" O   ILE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 147
    Processing helix  chain 'B' and resid 148 through 151
      removed outlier: 3.504A  pdb=" N   CYS B 151 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 148 through 151'
    Processing helix  chain 'B' and resid 157 through 165
    Processing helix  chain 'B' and resid 166 through 182
    Processing helix  chain 'B' and resid 196 through 210
    Processing helix  chain 'B' and resid 215 through 228
      removed outlier: 3.596A  pdb=" N   LYS B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 255
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 3.568A  pdb=" N   ALA B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 329
      removed outlier: 3.891A  pdb=" N   THR B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   SER B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      Proline residue:  B 308  - end of helix
    Processing helix  chain 'B' and resid 332 through 350
    Processing helix  chain 'B' and resid 357 through 366
    Processing helix  chain 'B' and resid 536 through 559
    Processing helix  chain 'B' and resid 562 through 594
    Processing helix  chain 'C' and resid 7 through 21
    Processing helix  chain 'C' and resid 29 through 41
    Processing helix  chain 'C' and resid 45 through 57
    Processing helix  chain 'C' and resid 66 through 74
    Processing helix  chain 'C' and resid 82 through 93
    Processing helix  chain 'C' and resid 103 through 111
    Processing helix  chain 'C' and resid 118 through 130
    Processing helix  chain 'C' and resid 139 through 148
    Processing helix  chain 'D' and resid 71 through 86
    Processing helix  chain 'D' and resid 90 through 114
    Processing helix  chain 'D' and resid 115 through 119
      removed outlier: 3.777A  pdb=" N   TYR D 118 " --> pdb=" O   ILE D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 147
    Processing helix  chain 'D' and resid 148 through 151
      removed outlier: 3.504A  pdb=" N   CYS D 151 " --> pdb=" O   ALA D 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 148 through 151'
    Processing helix  chain 'D' and resid 157 through 165
    Processing helix  chain 'D' and resid 166 through 182
    Processing helix  chain 'D' and resid 196 through 210
    Processing helix  chain 'D' and resid 215 through 228
      removed outlier: 3.595A  pdb=" N   LYS D 219 " --> pdb=" O   GLY D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 255
    Processing helix  chain 'D' and resid 263 through 276
      removed outlier: 3.567A  pdb=" N   ALA D 267 " --> pdb=" O   THR D 263 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 329
      removed outlier: 3.891A  pdb=" N   THR D 296 " --> pdb=" O   LEU D 292 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   SER D 303 " --> pdb=" O   LEU D 299 " (cutoff:3.500A)
      Proline residue:  D 308  - end of helix
    Processing helix  chain 'D' and resid 332 through 350
    Processing helix  chain 'D' and resid 357 through 366
    Processing helix  chain 'D' and resid 536 through 559
    Processing helix  chain 'D' and resid 562 through 594
    Processing helix  chain 'E' and resid 7 through 21
    Processing helix  chain 'E' and resid 29 through 41
    Processing helix  chain 'E' and resid 45 through 57
    Processing helix  chain 'E' and resid 66 through 74
    Processing helix  chain 'E' and resid 82 through 93
    Processing helix  chain 'E' and resid 103 through 111
    Processing helix  chain 'E' and resid 118 through 130
    Processing helix  chain 'E' and resid 139 through 148
    Processing helix  chain 'F' and resid 71 through 86
    Processing helix  chain 'F' and resid 90 through 114
    Processing helix  chain 'F' and resid 115 through 119
      removed outlier: 3.778A  pdb=" N   TYR F 118 " --> pdb=" O   ILE F 115 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 122 through 147
    Processing helix  chain 'F' and resid 148 through 151
      removed outlier: 3.504A  pdb=" N   CYS F 151 " --> pdb=" O   ALA F 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 148 through 151'
    Processing helix  chain 'F' and resid 157 through 165
    Processing helix  chain 'F' and resid 166 through 182
    Processing helix  chain 'F' and resid 196 through 210
    Processing helix  chain 'F' and resid 215 through 228
      removed outlier: 3.596A  pdb=" N   LYS F 219 " --> pdb=" O   GLY F 215 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 228 through 255
    Processing helix  chain 'F' and resid 263 through 276
      removed outlier: 3.568A  pdb=" N   ALA F 267 " --> pdb=" O   THR F 263 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 287 through 329
      removed outlier: 3.891A  pdb=" N   THR F 296 " --> pdb=" O   LEU F 292 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   SER F 303 " --> pdb=" O   LEU F 299 " (cutoff:3.500A)
      Proline residue:  F 308  - end of helix
    Processing helix  chain 'F' and resid 332 through 350
    Processing helix  chain 'F' and resid 357 through 366
    Processing helix  chain 'F' and resid 536 through 559
    Processing helix  chain 'F' and resid 562 through 594
    Processing helix  chain 'G' and resid 7 through 21
    Processing helix  chain 'G' and resid 29 through 41
    Processing helix  chain 'G' and resid 45 through 57
    Processing helix  chain 'G' and resid 66 through 74
    Processing helix  chain 'G' and resid 82 through 93
    Processing helix  chain 'G' and resid 103 through 111
    Processing helix  chain 'G' and resid 118 through 130
    Processing helix  chain 'G' and resid 139 through 148
    Processing sheet with id=AA1, first strand: chain 'H' and resid 27 through 28
    Processing sheet with id=AA2, first strand: chain 'H' and resid 100 through 102
      removed outlier: 3.670A  pdb=" N   ILE H 101 " --> pdb=" O   VAL H 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.670A  pdb=" N   ILE C 101 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 27 through 28
    Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 102
      removed outlier: 3.669A  pdb=" N   ILE E 101 " --> pdb=" O   VAL E 137 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 27 through 28
    Processing sheet with id=AA8, first strand: chain 'G' and resid 100 through 102
      removed outlier: 3.669A  pdb=" N   ILE G 101 " --> pdb=" O   VAL G 137 " (cutoff:3.500A)

    1185 hydrogen bonds defined for protein.
    3531 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2592
        1.30 -     1.43: 4474
        1.43 -     1.56: 9106
        1.56 -     1.68: 0
        1.68 -     1.81: 152
  Bond restraints: 16324
  Sorted by residual:
  bond pdb=" C12 GB9 B1001 "
       pdb=" N2  GB9 B1001 "
    ideal  model  delta    sigma   weight residual
    1.306  1.482 -0.176 2.00e-02 2.50e+03 7.74e+01
  bond pdb=" C12 GB9 F1001 "
       pdb=" N2  GB9 F1001 "
    ideal  model  delta    sigma   weight residual
    1.306  1.482 -0.176 2.00e-02 2.50e+03 7.74e+01
  bond pdb=" C12 GB9 A1001 "
       pdb=" N2  GB9 A1001 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.70e+01
  bond pdb=" C12 GB9 D1001 "
       pdb=" N2  GB9 D1001 "
    ideal  model  delta    sigma   weight residual
    1.306  1.481 -0.175 2.00e-02 2.50e+03 7.69e+01
  bond pdb=" C5  GB9 A1001 "
       pdb=" C8  GB9 A1001 "
    ideal  model  delta    sigma   weight residual
    1.386  1.529 -0.143 2.00e-02 2.50e+03 5.12e+01
  ... (remaining 16319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 21580
        1.90 -     3.80: 388
        3.80 -     5.70: 28
        5.70 -     7.60: 8
        7.60 -     9.50: 8
  Bond angle restraints: 22012
  Sorted by residual:
  angle pdb=" CA  LEU A 272 "
        pdb=" CB  LEU A 272 "
        pdb=" CG  LEU A 272 "
      ideal   model   delta    sigma   weight residual
     116.30  106.80    9.50 3.50e+00 8.16e-02 7.37e+00
  angle pdb=" CA  LEU B 272 "
        pdb=" CB  LEU B 272 "
        pdb=" CG  LEU B 272 "
      ideal   model   delta    sigma   weight residual
     116.30  106.83    9.47 3.50e+00 8.16e-02 7.32e+00
  angle pdb=" CA  LEU F 272 "
        pdb=" CB  LEU F 272 "
        pdb=" CG  LEU F 272 "
      ideal   model   delta    sigma   weight residual
     116.30  106.83    9.47 3.50e+00 8.16e-02 7.32e+00
  angle pdb=" CA  LEU D 272 "
        pdb=" CB  LEU D 272 "
        pdb=" CG  LEU D 272 "
      ideal   model   delta    sigma   weight residual
     116.30  106.89    9.41 3.50e+00 8.16e-02 7.23e+00
  angle pdb=" C2  GB9 D1001 "
        pdb=" N1  GB9 D1001 "
        pdb=" C3  GB9 D1001 "
      ideal   model   delta    sigma   weight residual
     128.33  120.50    7.83 3.00e+00 1.11e-01 6.81e+00
  ... (remaining 22007 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 8659
       17.86 -    35.71: 849
       35.71 -    53.57: 68
       53.57 -    71.42: 12
       71.42 -    89.28: 8
  Dihedral angle restraints: 9596
    sinusoidal: 3900
      harmonic: 5696
  Sorted by residual:
  dihedral pdb=" CA  SER D 122 "
           pdb=" C   SER D 122 "
           pdb=" N   GLU D 123 "
           pdb=" CA  GLU D 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  SER F 122 "
           pdb=" C   SER F 122 "
           pdb=" N   GLU F 123 "
           pdb=" CA  GLU F 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  SER B 122 "
           pdb=" C   SER B 122 "
           pdb=" N   GLU B 123 "
           pdb=" CA  GLU B 123 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.62  -19.38     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 9593 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1368
       0.025 -    0.049: 621
       0.049 -    0.074: 304
       0.074 -    0.098: 83
       0.098 -    0.123: 28
  Chirality restraints: 2404
  Sorted by residual:
  chirality pdb=" CA  PRO F 308 "
            pdb=" N   PRO F 308 "
            pdb=" C   PRO F 308 "
            pdb=" CB  PRO F 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  PRO B 308 "
            pdb=" N   PRO B 308 "
            pdb=" C   PRO B 308 "
            pdb=" CB  PRO B 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  PRO A 308 "
            pdb=" N   PRO A 308 "
            pdb=" C   PRO A 308 "
            pdb=" CB  PRO A 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.70e-01
  ... (remaining 2401 not shown)

  Planarity restraints: 2780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F 166 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.64e-01
        pdb=" N   PRO F 167 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO F 167 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO F 167 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 166 "   -0.016 5.00e-02 4.00e+02   2.45e-02 9.64e-01
        pdb=" N   PRO B 167 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO B 167 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 167 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 166 "    0.016 5.00e-02 4.00e+02   2.45e-02 9.62e-01
        pdb=" N   PRO D 167 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO D 167 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D 167 "    0.014 5.00e-02 4.00e+02
  ... (remaining 2777 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.45: 197
        2.45 -     3.06: 14779
        3.06 -     3.67: 28405
        3.67 -     4.29: 41579
        4.29 -     4.90: 59909
  Nonbonded interactions: 144869
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 571 "
            pdb=" O   VAL F 567 "
     model   vdw
     1.833 3.040
  nonbonded pdb=" NE2 GLN F 341 "
            pdb=" O   MET G 110 "
     model   vdw
     1.905 3.120
  nonbonded pdb=" OG  SER A 179 "
            pdb=" F1  GB9 A1001 "
     model   vdw
     1.973 2.990
  nonbonded pdb=" OG  SER B 179 "
            pdb=" F1  GB9 B1001 "
     model   vdw
     1.973 2.990
  nonbonded pdb=" OG  SER F 179 "
            pdb=" F1  GB9 F1001 "
     model   vdw
     1.973 2.990
  ... (remaining 144864 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.060
  Set scattering table:                    0.040
  Process input model:                     13.820
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
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      :  0.014   0.748  16328  Z= 1.236
  Angle     :  0.650   9.501  22012  Z= 0.384
  Chirality :  0.036   0.123   2404
  Planarity :  0.003   0.025   2780
  Dihedral  : 13.143  89.277   5932
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 102.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.16), residues: 1936
  helix: -1.78 (0.11), residues: 1484
  sheet:  None (None), residues: 0
  loop : -1.63 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 153 
 TYR   0.013   0.002   TYR D 571 
 PHE   0.012   0.002   PHE A 261 
 TRP   0.010   0.001   TRP A 146 
 HIS   0.007   0.002   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00773 (16324)
  covalent geometry    : angle       0.65038 (22012)
  hydrogen bonds       : bond        0.15387 ( 1185)
  hydrogen bonds       : angle       7.69404 ( 3531)
  Misc. bond           : bond        0.74773 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  390 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 390
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 ARG cc_start: 0.9215 (ttt90) cc_final: 0.8337 (ttt90)
REVERT: A  553 ARG cc_start: 0.9026 (mmp-170) cc_final: 0.8664 (mmp-170)
REVERT: B  174 MET cc_start: 0.8611 (ttt) cc_final: 0.8368 (tmm)
REVERT: B  293 LEU cc_start: 0.9482 (pp) cc_final: 0.9272 (pp)
REVERT: B  565 MET cc_start: 0.7017 (mtm) cc_final: 0.6605 (ttt)
REVERT: B  569 GLU cc_start: 0.9040 (pt0) cc_final: 0.8705 (mp0)
REVERT: D  172 ASP cc_start: 0.9075 (t70) cc_final: 0.8650 (t70)
REVERT: D  219 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8234 (mmtm)
REVERT: D  341 GLN cc_start: 0.8601 (mt0) cc_final: 0.8322 (mt0)
REVERT: D  565 MET cc_start: 0.7209 (mtm) cc_final: 0.6916 (ttt)
REVERT: F  174 MET cc_start: 0.8631 (ttt) cc_final: 0.8385 (tmm)
REVERT: F  565 MET cc_start: 0.7011 (mtm) cc_final: 0.6597 (ttt)
REVERT: F  569 GLU cc_start: 0.9055 (pt0) cc_final: 0.8695 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 390
  average time/residue: 0.1297
  time to fit residues: 73.5192
Evaluate side-chains
  282 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0570
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    5.4106

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

Flipped N/Q/H residues before XYZ refinement:
H  42 GLN
** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 328 HIS
C  42 GLN
** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 324 HIS
** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  42 GLN
** E 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 570 GLN
** G 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.119453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.077988 restraints weight = 66257.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.080100 restraints weight = 30587.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.081137 restraints weight = 19978.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.081669 restraints weight = 16164.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.081863 restraints weight = 14660.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16328  Z= 0.244
  Angle     :  0.721  12.486  22012  Z= 0.390
  Chirality :  0.044   0.202   2404
  Planarity :  0.005   0.043   2780
  Dihedral  :  4.806  22.670   2180
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 28.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.93 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.17), residues: 1936
  helix: -0.40 (0.12), residues: 1564
  sheet:  None (None), residues: 0
  loop : -1.37 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 144 
 TYR   0.021   0.002   TYR B 571 
 PHE   0.018   0.002   PHE A 297 
 TRP   0.008   0.001   TRP D 344 
 HIS   0.007   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (16324)
  covalent geometry    : angle       0.72133 (22012)
  hydrogen bonds       : bond        0.05585 ( 1185)
  hydrogen bonds       : angle       5.78400 ( 3531)
  Misc. bond           : bond        0.00199 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 354
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASN cc_start: 0.9639 (t0) cc_final: 0.9237 (p0)
REVERT: A  172 ASP cc_start: 0.9105 (t70) cc_final: 0.8826 (t0)
REVERT: A  273 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9106 (tp)
REVERT: B   83 ASN cc_start: 0.9647 (t0) cc_final: 0.9282 (p0)
REVERT: B  174 MET cc_start: 0.8897 (ttt) cc_final: 0.8548 (tmm)
REVERT: B  293 LEU cc_start: 0.9650 (pp) cc_final: 0.9431 (pp)
REVERT: D   83 ASN cc_start: 0.9624 (t0) cc_final: 0.9248 (p0)
REVERT: D  172 ASP cc_start: 0.9213 (t70) cc_final: 0.8710 (t0)
REVERT: D  273 ILE cc_start: 0.9607 (tt) cc_final: 0.9382 (tp)
REVERT: D  319 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8659 (tmtt)
REVERT: D  322 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8672 (mp0)
REVERT: E   91 ARG cc_start: 0.9167 (mtt180) cc_final: 0.8955 (mmt90)
REVERT: F   83 ASN cc_start: 0.9652 (t0) cc_final: 0.9281 (p0)
REVERT: F  174 MET cc_start: 0.8902 (ttt) cc_final: 0.8554 (tmm)
REVERT: F  293 LEU cc_start: 0.9652 (pp) cc_final: 0.9430 (pp)
REVERT: F  319 LYS cc_start: 0.8984 (tttt) cc_final: 0.8529 (tmtt)
REVERT: F  322 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8614 (mp0)
REVERT: F  323 GLN cc_start: 0.9076 (tp40) cc_final: 0.8621 (tp40)
REVERT: G   76 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8109 (tmtt)
REVERT: G   77 MET cc_start: 0.5925 (ptt) cc_final: 0.5351 (ptt)
REVERT: G   86 ILE cc_start: 0.8272 (tt) cc_final: 0.8026 (tt)
REVERT: G   91 ARG cc_start: 0.9170 (mtt180) cc_final: 0.8943 (mmt90)
REVERT: G  110 MET cc_start: 0.8383 (mmp) cc_final: 0.8121 (mmm)
REVERT: G  146 MET cc_start: 0.8584 (mtm) cc_final: 0.7601 (ptm)
  outliers start: 58
  outliers final: 33
  residues processed: 379
  average time/residue: 0.1151
  time to fit residues: 65.1199
Evaluate side-chains
  341 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 304
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 LEU
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  327 LYS
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  170 VAL
Chi-restraints excluded: chain D residue  233 VAL
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  585 LEU
Chi-restraints excluded: chain F residue  109 LEU
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  322 GLU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain F residue  328 HIS
Chi-restraints excluded: chain F residue  585 LEU
Chi-restraints excluded: chain G residue   76 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 141 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 133 optimal weight:    8.9990
   chunk 23 optimal weight:    0.8980
   chunk 188 optimal weight:    9.9990
   chunk 185 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 144 GLN
F 321 GLN
** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 144 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.120872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.079153 restraints weight = 65820.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.081371 restraints weight = 30234.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.082422 restraints weight = 19543.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.082644 restraints weight = 15735.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.082644 restraints weight = 14690.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  16328  Z= 0.211
  Angle     :  0.660   9.843  22012  Z= 0.358
  Chirality :  0.041   0.205   2404
  Planarity :  0.004   0.036   2780
  Dihedral  :  4.647  22.819   2180
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 24.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 16.37 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.18), residues: 1936
  helix:  0.27 (0.12), residues: 1560
  sheet:  None (None), residues: 0
  loop : -1.17 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 581 
 TYR   0.017   0.002   TYR B 571 
 PHE   0.016   0.002   PHE F 297 
 TRP   0.021   0.002   TRP B 288 
 HIS   0.009   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (16324)
  covalent geometry    : angle       0.65984 (22012)
  hydrogen bonds       : bond        0.04848 ( 1185)
  hydrogen bonds       : angle       5.30188 ( 3531)
  Misc. bond           : bond        0.00021 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 328
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 ASN cc_start: 0.9602 (t0) cc_final: 0.9152 (p0)
REVERT: A  172 ASP cc_start: 0.9082 (t70) cc_final: 0.8825 (t0)
REVERT: A  273 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9132 (tp)
REVERT: A  570 GLN cc_start: 0.8590 (tt0) cc_final: 0.8390 (tt0)
REVERT: H   52 MET cc_start: 0.0564 (mmm) cc_final: 0.0343 (mmt)
REVERT: H  101 ILE cc_start: 0.5449 (OUTLIER) cc_final: 0.4643 (mm)
REVERT: B  174 MET cc_start: 0.8920 (ttt) cc_final: 0.8522 (tmm)
REVERT: B  293 LEU cc_start: 0.9606 (pp) cc_final: 0.9390 (pp)
REVERT: C   52 MET cc_start: 0.0155 (mmt) cc_final: -0.0157 (mmt)
REVERT: C   93 PHE cc_start: 0.8438 (m-10) cc_final: 0.8185 (m-80)
REVERT: D   83 ASN cc_start: 0.9566 (t0) cc_final: 0.9078 (p0)
REVERT: D  172 ASP cc_start: 0.9098 (t70) cc_final: 0.8637 (t0)
REVERT: D  174 MET cc_start: 0.8937 (ttt) cc_final: 0.8623 (tmm)
REVERT: D  319 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8606 (tmtt)
REVERT: D  322 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8631 (mp0)
REVERT: E  101 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.4890 (mm)
REVERT: F  174 MET cc_start: 0.8944 (ttt) cc_final: 0.8536 (tmm)
REVERT: F  273 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9149 (tp)
REVERT: F  293 LEU cc_start: 0.9611 (pp) cc_final: 0.9402 (pp)
REVERT: F  319 LYS cc_start: 0.8986 (tttt) cc_final: 0.8466 (tmtt)
REVERT: F  322 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8501 (mp0)
REVERT: G   46 GLU cc_start: 0.8414 (pp20) cc_final: 0.8092 (mm-30)
REVERT: G   78 LYS cc_start: 0.9262 (pttp) cc_final: 0.9047 (ptpt)
  outliers start: 73
  outliers final: 48
  residues processed: 366
  average time/residue: 0.1186
  time to fit residues: 64.4147
Evaluate side-chains
  348 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 294
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain H residue  101 ILE
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  170 VAL
Chi-restraints excluded: chain D residue  202 PHE
Chi-restraints excluded: chain D residue  233 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  327 LYS
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  550 VAL
Chi-restraints excluded: chain D residue  585 LEU
Chi-restraints excluded: chain D residue  586 GLN
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  106 CYS
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  273 ILE
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  322 GLU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain F residue  328 HIS
Chi-restraints excluded: chain F residue  550 VAL
Chi-restraints excluded: chain F residue  585 LEU
Chi-restraints excluded: chain G residue  108 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 162 optimal weight:    9.9990
   chunk 48 optimal weight:   30.0000
   chunk 22 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 113 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    0.4980
   chunk 82 optimal weight:   10.0000
   chunk 136 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    5.8988

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

Flipped N/Q/H residues before XYZ refinement:
** H 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 144 GLN
** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.151939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.126614 restraints weight = 83252.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.128110 restraints weight = 35008.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.128821 restraints weight = 21679.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.128978 restraints weight = 17525.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.129243 restraints weight = 16569.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  16328  Z= 0.236
  Angle     :  0.680   9.089  22012  Z= 0.373
  Chirality :  0.042   0.220   2404
  Planarity :  0.004   0.049   2780
  Dihedral  :  4.695  22.202   2180
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 25.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 18.39 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.19), residues: 1936
  helix:  0.33 (0.12), residues: 1556
  sheet:  None (None), residues: 0
  loop : -0.95 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 581 
 TYR   0.019   0.002   TYR B 347 
 PHE   0.017   0.002   PHE A 297 
 TRP   0.010   0.001   TRP B 288 
 HIS   0.011   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 (16324)
  covalent geometry    : angle       0.67988 (22012)
  hydrogen bonds       : bond        0.04762 ( 1185)
  hydrogen bonds       : angle       5.21993 ( 3531)
  Misc. bond           : bond        0.00041 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  425 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 334
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.9111 (t70) cc_final: 0.8782 (t0)
REVERT: A  565 MET cc_start: 0.7759 (mmt) cc_final: 0.7493 (mmt)
REVERT: A  570 GLN cc_start: 0.8429 (tt0) cc_final: 0.7679 (tt0)
REVERT: H  101 ILE cc_start: 0.4551 (OUTLIER) cc_final: 0.3874 (mm)
REVERT: H  110 MET cc_start: 0.8191 (mmt) cc_final: 0.7967 (mmm)
REVERT: B  172 ASP cc_start: 0.9139 (t70) cc_final: 0.8644 (t0)
REVERT: B  174 MET cc_start: 0.8856 (ttt) cc_final: 0.8495 (tmm)
REVERT: C   52 MET cc_start: 0.0657 (mmt) cc_final: 0.0363 (mmt)
REVERT: C  101 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4081 (mm)
REVERT: D  172 ASP cc_start: 0.9073 (t70) cc_final: 0.8544 (t0)
REVERT: D  174 MET cc_start: 0.8912 (ttt) cc_final: 0.8559 (tmm)
REVERT: D  202 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8953 (m-80)
REVERT: D  231 GLU cc_start: 0.8789 (pm20) cc_final: 0.8529 (pm20)
REVERT: D  319 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8555 (tmtt)
REVERT: D  322 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8575 (mp0)
REVERT: D  565 MET cc_start: 0.7767 (mpp) cc_final: 0.7340 (mmt)
REVERT: D  570 GLN cc_start: 0.8436 (tt0) cc_final: 0.7800 (tt0)
REVERT: E  125 MET cc_start: 0.7920 (mtt) cc_final: 0.7516 (tpp)
REVERT: F  172 ASP cc_start: 0.9126 (t70) cc_final: 0.8666 (t0)
REVERT: F  174 MET cc_start: 0.8869 (ttt) cc_final: 0.8499 (tmm)
REVERT: F  231 GLU cc_start: 0.8842 (pm20) cc_final: 0.8557 (pm20)
REVERT: F  273 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9092 (tp)
REVERT: G   46 GLU cc_start: 0.8254 (pp20) cc_final: 0.7887 (mm-30)
REVERT: G  101 ILE cc_start: 0.4475 (OUTLIER) cc_final: 0.4195 (mp)
  outliers start: 91
  outliers final: 58
  residues processed: 380
  average time/residue: 0.1140
  time to fit residues: 64.9552
Evaluate side-chains
  367 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 303
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  101 ILE
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  327 LYS
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  106 CYS
Chi-restraints excluded: chain D residue  170 VAL
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  202 PHE
Chi-restraints excluded: chain D residue  233 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  322 GLU
Chi-restraints excluded: chain D residue  327 LYS
Chi-restraints excluded: chain D residue  328 HIS
Chi-restraints excluded: chain D residue  585 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  106 CYS
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  273 ILE
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain F residue  328 HIS
Chi-restraints excluded: chain F residue  585 LEU
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 147 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 165 optimal weight:    0.6980
   chunk 174 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 47 optimal weight:    6.9990
   chunk 142 optimal weight:    7.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 328 HIS
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 144 GLN
** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  42 GLN
E  43 ASN
** F 575 HIS ** 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 = 0.4564 r_free = 0.4564 target = 0.156575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.131325 restraints weight = 82766.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.132860 restraints weight = 35034.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.133761 restraints weight = 21934.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.134083 restraints weight = 17598.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.134083 restraints weight = 16242.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16328  Z= 0.157
  Angle     :  0.665   9.208  22012  Z= 0.356
  Chirality :  0.041   0.197   2404
  Planarity :  0.004   0.039   2780
  Dihedral  :  4.514  21.631   2180
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 20.42 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.19), residues: 1936
  helix:  0.69 (0.13), residues: 1560
  sheet:  None (None), residues: 0
  loop : -0.89 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 325 
 TYR   0.015   0.002   TYR F 347 
 PHE   0.017   0.002   PHE E  13 
 TRP   0.009   0.001   TRP D 344 
 HIS   0.009   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (16324)
  covalent geometry    : angle       0.66524 (22012)
  hydrogen bonds       : bond        0.04325 ( 1185)
  hydrogen bonds       : angle       4.97253 ( 3531)
  Misc. bond           : bond        0.00036 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 357
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.9409 (mt) cc_final: 0.9054 (pp)
REVERT: A  172 ASP cc_start: 0.9104 (t70) cc_final: 0.8833 (t70)
REVERT: A  570 GLN cc_start: 0.8804 (tt0) cc_final: 0.8537 (tt0)
REVERT: A  583 LYS cc_start: 0.9638 (mmtt) cc_final: 0.9277 (tptt)
REVERT: H   52 MET cc_start: 0.0258 (mmt) cc_final: -0.0003 (mmt)
REVERT: H  101 ILE cc_start: 0.4442 (OUTLIER) cc_final: 0.3665 (mm)
REVERT: B  172 ASP cc_start: 0.9066 (t70) cc_final: 0.8658 (t70)
REVERT: B  174 MET cc_start: 0.8906 (ttt) cc_final: 0.8437 (tmm)
REVERT: B  231 GLU cc_start: 0.8587 (pm20) cc_final: 0.8280 (pm20)
REVERT: C  101 ILE cc_start: 0.4408 (OUTLIER) cc_final: 0.3771 (mm)
REVERT: D  172 ASP cc_start: 0.9078 (t70) cc_final: 0.8626 (t0)
REVERT: D  174 MET cc_start: 0.8922 (ttt) cc_final: 0.8515 (tmm)
REVERT: D  202 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8953 (m-80)
REVERT: D  231 GLU cc_start: 0.8659 (pm20) cc_final: 0.8356 (pm20)
REVERT: D  319 LYS cc_start: 0.8910 (tmtt) cc_final: 0.8549 (tmtt)
REVERT: D  570 GLN cc_start: 0.8866 (tt0) cc_final: 0.8437 (tm-30)
REVERT: E   77 MET cc_start: 0.4355 (ptt) cc_final: 0.3981 (ptt)
REVERT: E  101 ILE cc_start: 0.4447 (OUTLIER) cc_final: 0.3924 (mm)
REVERT: E  110 MET cc_start: 0.8426 (mmp) cc_final: 0.8063 (mmm)
REVERT: E  146 MET cc_start: 0.7379 (mmm) cc_final: 0.6983 (mmm)
REVERT: F  172 ASP cc_start: 0.9075 (t70) cc_final: 0.8658 (t70)
REVERT: F  174 MET cc_start: 0.8928 (ttt) cc_final: 0.8461 (tmm)
REVERT: F  231 GLU cc_start: 0.8658 (pm20) cc_final: 0.8338 (pm20)
REVERT: G   46 GLU cc_start: 0.8196 (pp20) cc_final: 0.7983 (mm-30)
REVERT: G  101 ILE cc_start: 0.4438 (OUTLIER) cc_final: 0.3800 (mm)
  outliers start: 83
  outliers final: 56
  residues processed: 397
  average time/residue: 0.1156
  time to fit residues: 68.8528
Evaluate side-chains
  379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 318
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain H residue  101 ILE
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  327 LYS
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain D residue  106 CYS
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  202 PHE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  241 LEU
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  327 LYS
Chi-restraints excluded: chain D residue  585 LEU
Chi-restraints excluded: chain D residue  586 GLN
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  106 CYS
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain F residue  328 HIS
Chi-restraints excluded: chain F residue  585 LEU
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 133 optimal weight:    0.3980
   chunk 164 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 328 HIS
C  43 ASN
** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  43 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.132385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.088286 restraints weight = 58581.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.090817 restraints weight = 28439.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.092083 restraints weight = 18651.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.092390 restraints weight = 14883.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.092390 restraints weight = 13746.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  16328  Z= 0.142
  Angle     :  0.737  12.567  22012  Z= 0.370
  Chirality :  0.042   0.250   2404
  Planarity :  0.003   0.048   2780
  Dihedral  :  4.413  22.153   2180
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.44 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.19), residues: 1936
  helix:  0.93 (0.13), residues: 1564
  sheet:  None (None), residues: 0
  loop : -0.71 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 325 
 TYR   0.017   0.001   TYR A 237 
 PHE   0.025   0.002   PHE F 555 
 TRP   0.023   0.001   TRP D 288 
 HIS   0.009   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (16324)
  covalent geometry    : angle       0.73672 (22012)
  hydrogen bonds       : bond        0.04090 ( 1185)
  hydrogen bonds       : angle       4.79610 ( 3531)
  Misc. bond           : bond        0.00021 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  415 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 359
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.9459 (mt) cc_final: 0.9103 (pp)
REVERT: A  174 MET cc_start: 0.8917 (ttt) cc_final: 0.8498 (tmm)
REVERT: A  319 LYS cc_start: 0.8862 (tttt) cc_final: 0.8369 (tmtt)
REVERT: A  323 GLN cc_start: 0.8953 (tp40) cc_final: 0.8271 (tp40)
REVERT: A  570 GLN cc_start: 0.8824 (tt0) cc_final: 0.8602 (tt0)
REVERT: H   73 MET cc_start: 0.1857 (tpt) cc_final: 0.1474 (ptt)
REVERT: H  101 ILE cc_start: 0.4359 (OUTLIER) cc_final: 0.3627 (mm)
REVERT: H  125 MET cc_start: 0.7726 (mtt) cc_final: 0.7517 (ptp)
REVERT: H  146 MET cc_start: 0.6739 (mmm) cc_final: 0.6511 (mmm)
REVERT: B  172 ASP cc_start: 0.8998 (t70) cc_final: 0.8651 (t0)
REVERT: B  319 LYS cc_start: 0.8905 (tttt) cc_final: 0.8452 (tmtt)
REVERT: B  565 MET cc_start: 0.7149 (mmt) cc_final: 0.6932 (mmm)
REVERT: B  578 MET cc_start: 0.9017 (ptp) cc_final: 0.8689 (ptp)
REVERT: C   52 MET cc_start: 0.0252 (mmt) cc_final: -0.0017 (mmp)
REVERT: C  101 ILE cc_start: 0.4772 (OUTLIER) cc_final: 0.4101 (mm)
REVERT: C  146 MET cc_start: 0.7660 (mmm) cc_final: 0.7356 (mmm)
REVERT: D  172 ASP cc_start: 0.9019 (t70) cc_final: 0.8649 (t0)
REVERT: D  174 MET cc_start: 0.8991 (ttt) cc_final: 0.8511 (tmm)
REVERT: D  319 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8395 (tmtt)
REVERT: D  323 GLN cc_start: 0.8836 (tp40) cc_final: 0.8078 (tp40)
REVERT: E   77 MET cc_start: 0.3887 (ptt) cc_final: 0.3515 (ptt)
REVERT: E  146 MET cc_start: 0.7538 (mmm) cc_final: 0.7263 (mmm)
REVERT: F  172 ASP cc_start: 0.9039 (t70) cc_final: 0.8724 (t0)
REVERT: F  174 MET cc_start: 0.9001 (ttt) cc_final: 0.8477 (tmm)
REVERT: F  319 LYS cc_start: 0.8862 (tttt) cc_final: 0.8366 (tmtt)
REVERT: G  101 ILE cc_start: 0.4869 (OUTLIER) cc_final: 0.4230 (mm)
REVERT: G  146 MET cc_start: 0.7734 (mmm) cc_final: 0.7489 (mmm)
  outliers start: 56
  outliers final: 39
  residues processed: 393
  average time/residue: 0.1162
  time to fit residues: 68.1473
Evaluate side-chains
  346 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 304
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  101 ILE
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain D residue  585 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  109 LEU
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  299 LEU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 114 optimal weight:    9.9990
   chunk 47 optimal weight:   30.0000
   chunk 104 optimal weight:   20.0000
   chunk 60 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9980
   chunk 117 optimal weight:    8.9990
   chunk 165 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 95 optimal weight:   40.0000
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
H  43 ASN
** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.125581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.081957 restraints weight = 61679.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.084287 restraints weight = 28838.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.085395 restraints weight = 18646.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.085902 restraints weight = 14876.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.086196 restraints weight = 13536.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.6038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  16328  Z= 0.196
  Angle     :  0.776  12.215  22012  Z= 0.400
  Chirality :  0.045   0.220   2404
  Planarity :  0.004   0.073   2780
  Dihedral  :  4.638  27.737   2180
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 22.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.29 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.19), residues: 1936
  helix:  0.80 (0.13), residues: 1564
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 325 
 TYR   0.018   0.002   TYR F 347 
 PHE   0.026   0.002   PHE E  90 
 TRP   0.019   0.001   TRP D 288 
 HIS   0.004   0.001   HIS D 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (16324)
  covalent geometry    : angle       0.77622 (22012)
  hydrogen bonds       : bond        0.04423 ( 1185)
  hydrogen bonds       : angle       5.04646 ( 3531)
  Misc. bond           : bond        0.00042 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 318
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.9499 (mt) cc_final: 0.9192 (pp)
REVERT: A  137 PHE cc_start: 0.8982 (m-80) cc_final: 0.8775 (t80)
REVERT: A  201 ARG cc_start: 0.8905 (mmt180) cc_final: 0.8522 (mmt-90)
REVERT: A  570 GLN cc_start: 0.8804 (tt0) cc_final: 0.8589 (tt0)
REVERT: A  583 LYS cc_start: 0.9658 (mmtt) cc_final: 0.9318 (tptt)
REVERT: H   91 ARG cc_start: 0.8927 (mtm-85) cc_final: 0.8686 (mmt-90)
REVERT: H  136 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8948 (tp40)
REVERT: B  174 MET cc_start: 0.9028 (ttt) cc_final: 0.8523 (tmm)
REVERT: C   52 MET cc_start: 0.0527 (mmt) cc_final: 0.0134 (mmp)
REVERT: C  101 ILE cc_start: 0.4954 (OUTLIER) cc_final: 0.4273 (mm)
REVERT: D  174 MET cc_start: 0.9015 (ttt) cc_final: 0.8579 (tmm)
REVERT: D  319 LYS cc_start: 0.8737 (tmtt) cc_final: 0.8287 (tmtt)
REVERT: D  323 GLN cc_start: 0.8848 (tp40) cc_final: 0.8223 (tp40)
REVERT: D  570 GLN cc_start: 0.8883 (tt0) cc_final: 0.8611 (tm-30)
REVERT: D  578 MET cc_start: 0.9155 (ptp) cc_final: 0.8883 (ptp)
REVERT: D  585 LEU cc_start: 0.8645 (tt) cc_final: 0.8404 (mt)
REVERT: E   72 MET cc_start: 0.5260 (ptm) cc_final: 0.4814 (ptt)
REVERT: E   77 MET cc_start: 0.3942 (ptt) cc_final: 0.3634 (ptt)
REVERT: E  101 ILE cc_start: 0.4856 (OUTLIER) cc_final: 0.4185 (mm)
REVERT: F  172 ASP cc_start: 0.9122 (t70) cc_final: 0.8766 (t0)
REVERT: F  174 MET cc_start: 0.9035 (ttt) cc_final: 0.8529 (tmm)
REVERT: F  570 GLN cc_start: 0.8897 (tt0) cc_final: 0.8552 (tm-30)
REVERT: G  101 ILE cc_start: 0.5116 (OUTLIER) cc_final: 0.4481 (mm)
  outliers start: 65
  outliers final: 54
  residues processed: 356
  average time/residue: 0.1199
  time to fit residues: 63.2326
Evaluate side-chains
  357 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 300
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  575 HIS
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 ASP
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  327 LYS
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  247 SER
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  266 ASP
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  299 LEU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 75 optimal weight:   50.0000
   chunk 27 optimal weight:   50.0000
   chunk 144 optimal weight:   30.0000
   chunk 33 optimal weight:    6.9990
   chunk 95 optimal weight:   30.0000
   chunk 98 optimal weight:   10.0000
   chunk 73 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 170 optimal weight:    8.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
B 328 HIS
** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.123343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.081123 restraints weight = 64056.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.082724 restraints weight = 39307.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.083289 restraints weight = 21286.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.083386 restraints weight = 20292.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.083476 restraints weight = 18428.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.6037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  16328  Z= 0.244
  Angle     :  0.806  13.374  22012  Z= 0.421
  Chirality :  0.045   0.298   2404
  Planarity :  0.004   0.039   2780
  Dihedral  :  4.865  25.206   2180
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 25.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 24.70 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.19), residues: 1936
  helix:  0.61 (0.13), residues: 1560
  sheet:  None (None), residues: 0
  loop : -0.56 (0.35), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 325 
 TYR   0.022   0.002   TYR B 237 
 PHE   0.032   0.002   PHE A 548 
 TRP   0.019   0.002   TRP D 288 
 HIS   0.006   0.001   HIS D 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 (16324)
  covalent geometry    : angle       0.80593 (22012)
  hydrogen bonds       : bond        0.04629 ( 1185)
  hydrogen bonds       : angle       5.25343 ( 3531)
  Misc. bond           : bond        0.00020 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 308
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.9572 (mt) cc_final: 0.9298 (pp)
REVERT: A  174 MET cc_start: 0.8993 (ttt) cc_final: 0.8626 (tmm)
REVERT: A  231 GLU cc_start: 0.8738 (pm20) cc_final: 0.8407 (pm20)
REVERT: A  570 GLN cc_start: 0.8821 (tt0) cc_final: 0.8611 (tt0)
REVERT: H   91 ARG cc_start: 0.8855 (mtm-85) cc_final: 0.8612 (mmt180)
REVERT: H  125 MET cc_start: 0.7956 (mtt) cc_final: 0.7282 (tpt)
REVERT: B   81 LEU cc_start: 0.9616 (mt) cc_final: 0.9375 (pp)
REVERT: C   52 MET cc_start: 0.0486 (mmt) cc_final: 0.0062 (mmp)
REVERT: C   77 MET cc_start: 0.4503 (ptt) cc_final: 0.4143 (ttp)
REVERT: C  101 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.3732 (mm)
REVERT: D  174 MET cc_start: 0.9003 (ttt) cc_final: 0.8587 (tmm)
REVERT: D  201 ARG cc_start: 0.8938 (mmt-90) cc_final: 0.8667 (mmt180)
REVERT: D  248 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7800 (t80)
REVERT: D  319 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8254 (tmtt)
REVERT: D  323 GLN cc_start: 0.8934 (tp40) cc_final: 0.8386 (tp40)
REVERT: D  578 MET cc_start: 0.9183 (ptp) cc_final: 0.8971 (ptp)
REVERT: D  585 LEU cc_start: 0.8827 (tt) cc_final: 0.8595 (mt)
REVERT: E   37 MET cc_start: 0.7129 (tmm) cc_final: 0.6263 (ppp)
REVERT: E   77 MET cc_start: 0.4052 (ptt) cc_final: 0.3664 (ptt)
REVERT: E  101 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4379 (mm)
REVERT: E  146 MET cc_start: 0.6722 (mmm) cc_final: 0.6466 (mmm)
REVERT: F  570 GLN cc_start: 0.8855 (tt0) cc_final: 0.8512 (tm-30)
REVERT: F  583 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9307 (tmtt)
REVERT: G   77 MET cc_start: 0.4991 (ptt) cc_final: 0.4736 (ttp)
REVERT: G  101 ILE cc_start: 0.5512 (OUTLIER) cc_final: 0.4934 (mm)
  outliers start: 71
  outliers final: 53
  residues processed: 352
  average time/residue: 0.1167
  time to fit residues: 60.7989
Evaluate side-chains
  359 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 302
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 ASP
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  106 CYS
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  247 SER
Chi-restraints excluded: chain D residue  248 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   31 LYS
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  106 CYS
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  233 VAL
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  266 ASP
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  296 THR
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 77 optimal weight:   30.0000
   chunk 18 optimal weight:    5.9990
   chunk 186 optimal weight:    1.9990
   chunk 124 optimal weight:   30.0000
   chunk 173 optimal weight:   20.0000
   chunk 126 optimal weight:    5.9990
   chunk 141 optimal weight:    8.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.125297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.081989 restraints weight = 62869.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.084251 restraints weight = 29856.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.085304 restraints weight = 19709.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.085835 restraints weight = 15936.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.085984 restraints weight = 14533.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.6376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  16328  Z= 0.196
  Angle     :  0.809  13.487  22012  Z= 0.417
  Chirality :  0.045   0.277   2404
  Planarity :  0.004   0.049   2780
  Dihedral  :  4.831  26.813   2180
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 23.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 26.13 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.19), residues: 1936
  helix:  0.71 (0.13), residues: 1556
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  91 
 TYR   0.021   0.002   TYR B 237 
 PHE   0.018   0.002   PHE F 555 
 TRP   0.018   0.001   TRP D 288 
 HIS   0.005   0.001   HIS D 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (16324)
  covalent geometry    : angle       0.80850 (22012)
  hydrogen bonds       : bond        0.04450 ( 1185)
  hydrogen bonds       : angle       5.15972 ( 3531)
  Misc. bond           : bond        0.00019 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 323
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LEU cc_start: 0.9538 (mt) cc_final: 0.9239 (pp)
REVERT: A  174 MET cc_start: 0.8950 (ttt) cc_final: 0.8582 (tmm)
REVERT: A  201 ARG cc_start: 0.9067 (mmt180) cc_final: 0.8643 (mmt-90)
REVERT: A  231 GLU cc_start: 0.8561 (pm20) cc_final: 0.8226 (pm20)
REVERT: A  341 GLN cc_start: 0.9097 (mt0) cc_final: 0.8865 (tt0)
REVERT: A  570 GLN cc_start: 0.8793 (tt0) cc_final: 0.8579 (tt0)
REVERT: H   73 MET cc_start: 0.1961 (tpt) cc_final: 0.1485 (ptt)
REVERT: H   91 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8503 (mmt180)
REVERT: H  125 MET cc_start: 0.7805 (mtt) cc_final: 0.6992 (tpt)
REVERT: B  319 LYS cc_start: 0.8845 (tttt) cc_final: 0.8323 (tmtt)
REVERT: B  323 GLN cc_start: 0.8949 (tp40) cc_final: 0.8263 (tp40)
REVERT: C   52 MET cc_start: 0.0442 (mmt) cc_final: 0.0047 (mmp)
REVERT: C  101 ILE cc_start: 0.4970 (OUTLIER) cc_final: 0.4246 (mm)
REVERT: D  201 ARG cc_start: 0.8886 (mmt-90) cc_final: 0.8666 (mmt-90)
REVERT: D  248 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7719 (t80)
REVERT: D  319 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8271 (tmtt)
REVERT: D  323 GLN cc_start: 0.8873 (tp40) cc_final: 0.8336 (tp40)
REVERT: D  570 GLN cc_start: 0.8882 (tt0) cc_final: 0.8608 (tm-30)
REVERT: D  578 MET cc_start: 0.9109 (ptp) cc_final: 0.8812 (ptp)
REVERT: E   37 MET cc_start: 0.7075 (tmm) cc_final: 0.6288 (ppp)
REVERT: E   72 MET cc_start: 0.5248 (ptm) cc_final: 0.4843 (ptt)
REVERT: E   77 MET cc_start: 0.4254 (ptt) cc_final: 0.3765 (ptt)
REVERT: E  101 ILE cc_start: 0.4857 (OUTLIER) cc_final: 0.4241 (mm)
REVERT: E  125 MET cc_start: 0.7780 (mtt) cc_final: 0.7562 (ptp)
REVERT: E  146 MET cc_start: 0.6262 (mmm) cc_final: 0.5904 (mmm)
REVERT: G   73 MET cc_start: 0.1661 (tpt) cc_final: 0.1349 (ptt)
REVERT: G   77 MET cc_start: 0.4764 (ptt) cc_final: 0.4413 (ttp)
REVERT: G  101 ILE cc_start: 0.5298 (OUTLIER) cc_final: 0.4696 (mm)
  outliers start: 60
  outliers final: 48
  residues processed: 359
  average time/residue: 0.1216
  time to fit residues: 64.9064
Evaluate side-chains
  358 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 306
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  142 PHE
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  142 PHE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  248 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 170 optimal weight:    9.9990
   chunk 191 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 173 optimal weight:    9.9990
   chunk 85 optimal weight:   20.0000
   chunk 100 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 575 HIS
** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.156038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.133870 restraints weight = 82557.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.133101 restraints weight = 37551.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.133752 restraints weight = 28031.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.133695 restraints weight = 24068.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.133825 restraints weight = 24310.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.6564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  16328  Z= 0.184
  Angle     :  0.848  14.575  22012  Z= 0.433
  Chirality :  0.046   0.445   2404
  Planarity :  0.004   0.046   2780
  Dihedral  :  4.819  26.817   2180
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 23.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.67 %
    Favored  : 70.12 %
  Cbeta Deviations :  0.05 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.19), residues: 1936
  helix:  0.76 (0.13), residues: 1556
  sheet:  None (None), residues: 0
  loop : -0.51 (0.35), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 325 
 TYR   0.022   0.002   TYR B 571 
 PHE   0.018   0.002   PHE D 240 
 TRP   0.017   0.001   TRP D 288 
 HIS   0.006   0.001   HIS B 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (16324)
  covalent geometry    : angle       0.84823 (22012)
  hydrogen bonds       : bond        0.04389 ( 1185)
  hydrogen bonds       : angle       5.15632 ( 3531)
  Misc. bond           : bond        0.00015 (    4)

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

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

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3872 Ramachandran restraints generated.
    1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 320
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8877 (ttt) cc_final: 0.8498 (tmm)
REVERT: A  201 ARG cc_start: 0.9008 (mmt180) cc_final: 0.8650 (mmt-90)
REVERT: A  231 GLU cc_start: 0.8707 (pm20) cc_final: 0.8266 (pm20)
REVERT: A  341 GLN cc_start: 0.8764 (mt0) cc_final: 0.8397 (tt0)
REVERT: A  570 GLN cc_start: 0.8709 (tt0) cc_final: 0.8369 (tt0)
REVERT: H   73 MET cc_start: 0.2373 (tpt) cc_final: 0.1871 (ptt)
REVERT: H   91 ARG cc_start: 0.8692 (mtm-85) cc_final: 0.8472 (mmt180)
REVERT: B  327 LYS cc_start: 0.8501 (pttt) cc_final: 0.8271 (pttp)
REVERT: C   52 MET cc_start: 0.1176 (mmt) cc_final: 0.0518 (mmp)
REVERT: C   73 MET cc_start: 0.2404 (tpt) cc_final: 0.2005 (ptt)
REVERT: C   77 MET cc_start: 0.4647 (ptt) cc_final: 0.4395 (ttp)
REVERT: C  101 ILE cc_start: 0.3679 (OUTLIER) cc_final: 0.2988 (mm)
REVERT: C  125 MET cc_start: 0.6975 (ptp) cc_final: 0.6579 (tpp)
REVERT: D  248 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7843 (t80)
REVERT: D  319 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8597 (tmtt)
REVERT: D  323 GLN cc_start: 0.8901 (tp40) cc_final: 0.8547 (tp40)
REVERT: D  570 GLN cc_start: 0.8761 (tt0) cc_final: 0.8334 (tm-30)
REVERT: E   37 MET cc_start: 0.6526 (tmm) cc_final: 0.5660 (ppp)
REVERT: E   72 MET cc_start: 0.4914 (ptm) cc_final: 0.4265 (ptt)
REVERT: E   77 MET cc_start: 0.4413 (ptt) cc_final: 0.3878 (ptt)
REVERT: E  101 ILE cc_start: 0.3663 (OUTLIER) cc_final: 0.2956 (mm)
REVERT: E  125 MET cc_start: 0.7236 (mtt) cc_final: 0.6960 (ptp)
REVERT: E  146 MET cc_start: 0.5949 (mmm) cc_final: 0.5655 (mmm)
REVERT: F  197 LEU cc_start: 0.9043 (tp) cc_final: 0.8663 (mm)
REVERT: F  201 ARG cc_start: 0.8922 (mmt180) cc_final: 0.8575 (mmt-90)
REVERT: G   73 MET cc_start: 0.2124 (tpt) cc_final: 0.1853 (ptt)
REVERT: G   77 MET cc_start: 0.5022 (ptt) cc_final: 0.4707 (ttp)
REVERT: G  101 ILE cc_start: 0.3900 (OUTLIER) cc_final: 0.3440 (mm)
REVERT: G  125 MET cc_start: 0.7183 (ptp) cc_final: 0.6809 (tpp)
  outliers start: 54
  outliers final: 48
  residues processed: 348
  average time/residue: 0.1210
  time to fit residues: 62.1615
Evaluate side-chains
  363 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 311
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  202 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  327 LYS
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   88 GLU
Chi-restraints excluded: chain H residue  108 HIS
Chi-restraints excluded: chain H residue  147 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  142 PHE
Chi-restraints excluded: chain B residue  202 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  244 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  266 ASP
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  108 HIS
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  243 LEU
Chi-restraints excluded: chain D residue  248 PHE
Chi-restraints excluded: chain D residue  263 THR
Chi-restraints excluded: chain D residue  268 LEU
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue  101 ILE
Chi-restraints excluded: chain E residue  108 HIS
Chi-restraints excluded: chain E residue  147 THR
Chi-restraints excluded: chain F residue  106 CYS
Chi-restraints excluded: chain F residue  142 PHE
Chi-restraints excluded: chain F residue  202 PHE
Chi-restraints excluded: chain F residue  243 LEU
Chi-restraints excluded: chain F residue  263 THR
Chi-restraints excluded: chain F residue  266 ASP
Chi-restraints excluded: chain F residue  268 LEU
Chi-restraints excluded: chain F residue  292 LEU
Chi-restraints excluded: chain F residue  303 SER
Chi-restraints excluded: chain F residue  327 LYS
Chi-restraints excluded: chain G residue   30 THR
Chi-restraints excluded: chain G residue  101 ILE
Chi-restraints excluded: chain G residue  108 HIS
Chi-restraints excluded: chain G residue  147 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 192
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 173 optimal weight:   30.0000
   chunk 137 optimal weight:    4.9990
   chunk 162 optimal weight:    9.9990
   chunk 163 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 75 optimal weight:   30.0000
   chunk 26 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    4.5588

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

Flipped N/Q/H residues before XYZ refinement:
** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 341 GLN
** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.154468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.131906 restraints weight = 82002.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.131668 restraints weight = 48016.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.132098 restraints weight = 28824.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.132253 restraints weight = 26830.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.132309 restraints weight = 22997.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.6690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  16328  Z= 0.207
  Angle     :  0.869  14.226  22012  Z= 0.446
  Chirality :  0.048   0.545   2404
  Planarity :  0.004   0.080   2780
  Dihedral  :  4.867  26.167   2180
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 24.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.61 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.19), residues: 1936
  helix:  0.71 (0.13), residues: 1536
  sheet:  None (None), residues: 0
  loop : -0.55 (0.34), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 325 
 TYR   0.020   0.002   TYR B 237 
 PHE   0.035   0.002   PHE A 548 
 TRP   0.018   0.001   TRP D 288 
 HIS   0.010   0.001   HIS B 575 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (16324)
  covalent geometry    : angle       0.86947 (22012)
  hydrogen bonds       : bond        0.04518 ( 1185)
  hydrogen bonds       : angle       5.23979 ( 3531)
  Misc. bond           : bond        0.00019 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3077.12 seconds
wall clock time: 54 minutes 1.88 seconds (3241.88 seconds total)