Starting phenix.real_space_refine
on Sat Dec 28 18:39:22 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wwn_37894/12_2024/8wwn_37894.cif"
  }
  resolution = 2.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.084
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    5705      2.51       5
     N    1517      2.21       5
     O    1670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8960
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1749
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 2622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2622
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 5, 'TRANS': 336}
    Chain: "C"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "E"
      Number of atoms: 1779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1779
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2235
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 32
    Chain: "L"
      Number of atoms: 139
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 139
          Classifications: {'peptide': 17}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 15}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 5.17, per 1000 atoms: 0.58
  Number of scatterers: 8960
  At special positions: 0
  Unit cell: (87.74, 116.63, 125.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      68     16.00
     O    1670      8.00
     N    1517      7.00
     C    5705      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 185 " - pdb=" SG  CYS R 263 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   7 " - pdb=" SG  CYS L  16 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.13
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      37.8% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.559A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.525A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.346A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.900A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.027A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.130A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 7 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'R' and resid 108 through 138
      Proline residue:  R 113  - end of helix
    Processing helix  chain 'R' and resid 145 through 164
    Processing helix  chain 'R' and resid 165 through 174
      removed outlier: 6.120A  pdb=" N   GLN R 171 " --> pdb=" O   PHE R 167 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   LEU R 172 " --> pdb=" O   MET R 168 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET R 173 " --> pdb=" O   ILE R 169 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLY R 174 " --> pdb=" O   HIS R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 216
      removed outlier: 3.779A  pdb=" N   MET R 184 " --> pdb=" O   PHE R 180 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 223
      removed outlier: 3.681A  pdb=" N   LYS R 222 " --> pdb=" O   SER R 219 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 225 through 244
    Processing helix  chain 'R' and resid 244 through 250
      removed outlier: 3.569A  pdb=" N   TYR R 250 " --> pdb=" O   PRO R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 273 through 286
    Processing helix  chain 'R' and resid 286 through 303
    Processing helix  chain 'R' and resid 313 through 348
      Proline residue:  R 340  - end of helix
    Processing helix  chain 'R' and resid 355 through 384
      removed outlier: 4.202A  pdb=" N   SER R 373 " --> pdb=" O   GLY R 369 " (cutoff:3.500A)
      Proline residue:  R 377  - end of helix
      removed outlier: 3.524A  pdb=" N   CYS R 384 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 384 through 395
      removed outlier: 3.501A  pdb=" N   SER R 394 " --> pdb=" O   ARG R 390 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.310A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.698A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.544A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 5.947A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.627A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.683A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.385A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.679A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12
      removed outlier: 6.714A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 4.240A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.443A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255
    Processing sheet with id=AB6, first strand: chain 'L' and resid 8 through 9
      removed outlier: 3.663A  pdb=" N   VAL L  12 " --> pdb=" O   LEU L   9 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1311 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: 2.86

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2890
        1.34 -     1.46: 2125
        1.46 -     1.58: 4037
        1.58 -     1.69: 0
        1.69 -     1.81: 99
  Bond restraints: 9151
  Sorted by residual:
  bond pdb=" CG1 ILE B 273 "
       pdb=" CD1 ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.513  1.486  0.027 3.90e-02 6.57e+02 4.67e-01
  bond pdb=" C   ALA E 241 "
       pdb=" N   GLY E 242 "
    ideal  model  delta    sigma   weight residual
    1.331  1.321  0.010 1.46e-02 4.69e+03 4.65e-01
  bond pdb=" CA  PRO R 310 "
       pdb=" C   PRO R 310 "
    ideal  model  delta    sigma   weight residual
    1.527  1.520  0.007 1.07e-02 8.73e+03 4.53e-01
  bond pdb=" C   LEU A  39 "
       pdb=" N   GLY A  40 "
    ideal  model  delta    sigma   weight residual
    1.331  1.321  0.009 1.46e-02 4.69e+03 3.93e-01
  bond pdb=" CG  PRO R 217 "
       pdb=" CD  PRO R 217 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.67e-01
  ... (remaining 9146 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.09: 12098
        1.09 -     2.18: 254
        2.18 -     3.28: 50
        3.28 -     4.37: 7
        4.37 -     5.46: 11
  Bond angle restraints: 12420
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  110.08    3.12 9.60e-01 1.09e+00 1.05e+01
  angle pdb=" C   ASN R 145 "
        pdb=" N   VAL R 146 "
        pdb=" CA  VAL R 146 "
      ideal   model   delta    sigma   weight residual
     120.33  122.64   -2.31 8.00e-01 1.56e+00 8.33e+00
  angle pdb=" C   ASP B 333 "
        pdb=" N   SER B 334 "
        pdb=" CA  SER B 334 "
      ideal   model   delta    sigma   weight residual
     122.74  125.99   -3.25 1.44e+00 4.82e-01 5.08e+00
  angle pdb=" C   ARG E 191 "
        pdb=" N   MET E 192 "
        pdb=" CA  MET E 192 "
      ideal   model   delta    sigma   weight residual
     121.54  125.71   -4.17 1.91e+00 2.74e-01 4.77e+00
  angle pdb=" C   VAL R 146 "
        pdb=" CA  VAL R 146 "
        pdb=" CB  VAL R 146 "
      ideal   model   delta    sigma   weight residual
     114.00  111.23    2.77 1.31e+00 5.83e-01 4.48e+00
  ... (remaining 12415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 5236
       17.93 -    35.86: 152
       35.86 -    53.80: 30
       53.80 -    71.73: 2
       71.73 -    89.66: 2
  Dihedral angle restraints: 5422
    sinusoidal: 2056
      harmonic: 3366
  Sorted by residual:
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.00   17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.56   16.44     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5419 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 859
       0.028 -    0.055: 362
       0.055 -    0.083: 112
       0.083 -    0.110: 74
       0.110 -    0.138: 18
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" CA  ILE E 189 "
            pdb=" N   ILE E 189 "
            pdb=" C   ILE E 189 "
            pdb=" CB  ILE E 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ILE B 338 "
            pdb=" N   ILE B 338 "
            pdb=" C   ILE B 338 "
            pdb=" CB  ILE B 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1422 not shown)

  Planarity restraints: 1571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO B 236 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 106 "   -0.022 5.00e-02 4.00e+02   3.29e-02 1.74e+00
        pdb=" N   PRO E 107 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO E 107 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E 107 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.020 5.00e-02 4.00e+02   2.95e-02 1.40e+00
        pdb=" N   PRO B 194 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1568 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 383
        2.72 -     3.27: 8868
        3.27 -     3.81: 15152
        3.81 -     4.36: 19541
        4.36 -     4.90: 33044
  Nonbonded interactions: 76988
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 175 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   SER R 243 "
            pdb=" OH  TYR R 280 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLN R 171 "
            pdb=" OH  TYR L  13 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.289 3.040
  ... (remaining 76983 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.580
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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      :  0.002   0.027   9151  Z= 0.148
  Angle     :  0.442   5.461  12420  Z= 0.245
  Chirality :  0.040   0.138   1425
  Planarity :  0.003   0.053   1571
  Dihedral  :  9.194  89.661   3238
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  4.34 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1144
  helix:  0.79 (0.25), residues: 393
  sheet:  0.74 (0.29), residues: 298
  loop :  0.48 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.009   0.001   TYR E 103 
 ARG   0.003   0.000   ARG E  38 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 184
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7882 (ttm170)
REVERT: A   22 ASN cc_start: 0.8404 (m-40) cc_final: 0.8174 (m110)
REVERT: A   24 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7444 (mtm110)
REVERT: A  208 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7600 (ttm110)
REVERT: A  312 LYS cc_start: 0.8286 (tppt) cc_final: 0.8071 (mptt)
REVERT: B   25 CYS cc_start: 0.8459 (p) cc_final: 0.8221 (p)
REVERT: B  124 TYR cc_start: 0.9084 (m-80) cc_final: 0.8814 (m-80)
REVERT: B  137 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8103 (mmt90)
REVERT: B  138 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: E   30 SER cc_start: 0.8794 (p) cc_final: 0.8571 (m)
REVERT: E   46 GLU cc_start: 0.8234 (tt0) cc_final: 0.8030 (tt0)
REVERT: R  239 LEU cc_start: 0.7679 (mt) cc_final: 0.7350 (tp)
REVERT: R  266 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7236 (mtm110)
REVERT: R  325 ARG cc_start: 0.7348 (ptt-90) cc_final: 0.6865 (ptt-90)
  outliers start: 6
  outliers final: 3
  residues processed: 188
  average time/residue: 1.3747
  time to fit residues: 274.1316
Evaluate side-chains
  153 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain R residue  280 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 GLN
A 322 HIS
A 333 GLN
B 220 GLN
E   3 GLN
R 281 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9151  Z= 0.223
  Angle     :  0.537   6.114  12420  Z= 0.293
  Chirality :  0.043   0.150   1425
  Planarity :  0.004   0.054   1571
  Dihedral  :  4.893  55.407   1257
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.62 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1144
  helix:  2.05 (0.26), residues: 397
  sheet:  0.68 (0.29), residues: 301
  loop :  0.25 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.013   0.001   TYR R 341 
 ARG   0.003   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 155
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7914 (ttp-110)
REVERT: A   22 ASN cc_start: 0.8337 (m-40) cc_final: 0.8048 (m-40)
REVERT: A   24 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7406 (mtt90)
REVERT: A   46 LYS cc_start: 0.7588 (ttpm) cc_final: 0.7276 (ttpt)
REVERT: A  208 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7617 (ttm110)
REVERT: A  305 CYS cc_start: 0.8235 (m) cc_final: 0.7949 (t)
REVERT: A  312 LYS cc_start: 0.8311 (tppt) cc_final: 0.8038 (mptt)
REVERT: B  124 TYR cc_start: 0.9036 (m-80) cc_final: 0.8785 (m-80)
REVERT: B  197 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7187 (mtt-85)
REVERT: C   21 MET cc_start: 0.7466 (mmm) cc_final: 0.6900 (tmm)
REVERT: R  165 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7619 (ttt)
REVERT: R  235 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (tt)
REVERT: R  239 LEU cc_start: 0.7371 (mt) cc_final: 0.7098 (tp)
REVERT: R  266 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7390 (mtm110)
  outliers start: 29
  outliers final: 10
  residues processed: 163
  average time/residue: 1.4466
  time to fit residues: 249.3400
Evaluate side-chains
  158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 85 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 304 GLN
B 259 GLN
E   3 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9151  Z= 0.203
  Angle     :  0.504   5.159  12420  Z= 0.274
  Chirality :  0.042   0.147   1425
  Planarity :  0.004   0.055   1571
  Dihedral  :  4.465  50.404   1255
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 10.44 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1144
  helix:  2.34 (0.26), residues: 396
  sheet:  0.47 (0.29), residues: 309
  loop :  0.19 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.012   0.001   TYR E 103 
 ARG   0.003   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7925 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7433 (mtm-85)
REVERT: A  208 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7575 (ttm110)
REVERT: A  304 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (tm-30)
REVERT: A  305 CYS cc_start: 0.8231 (m) cc_final: 0.7966 (t)
REVERT: A  312 LYS cc_start: 0.8261 (tppt) cc_final: 0.8044 (mptt)
REVERT: C   21 MET cc_start: 0.7521 (mmm) cc_final: 0.6992 (tmm)
REVERT: R  165 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7725 (ttt)
REVERT: R  235 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (tt)
REVERT: R  239 LEU cc_start: 0.7336 (mt) cc_final: 0.7073 (tp)
REVERT: R  252 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.5722 (mpp80)
  outliers start: 34
  outliers final: 13
  residues processed: 165
  average time/residue: 1.3786
  time to fit residues: 241.2521
Evaluate side-chains
  158 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  304 GLN
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
R 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9151  Z= 0.312
  Angle     :  0.561   6.150  12420  Z= 0.302
  Chirality :  0.044   0.149   1425
  Planarity :  0.004   0.058   1571
  Dihedral  :  4.630  51.048   1254
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 11.38 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1144
  helix:  2.24 (0.26), residues: 397
  sheet:  0.32 (0.28), residues: 309
  loop :  0.01 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.022   0.002   PHE B 151 
 TYR   0.018   0.002   TYR E 103 
 ARG   0.004   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8208 (ttm170) cc_final: 0.8000 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7507 (mtm-85)
REVERT: A  208 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7548 (ttm110)
REVERT: A  209 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7800 (ptmm)
REVERT: A  305 CYS cc_start: 0.8257 (m) cc_final: 0.7989 (t)
REVERT: A  312 LYS cc_start: 0.8257 (tppt) cc_final: 0.8039 (mptt)
REVERT: B  217 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.7569 (pmt)
REVERT: C   21 MET cc_start: 0.7521 (mmm) cc_final: 0.7016 (tmm)
REVERT: R  165 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7860 (ttt)
REVERT: R  235 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: R  239 LEU cc_start: 0.7320 (mt) cc_final: 0.7070 (tp)
REVERT: R  252 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5782 (mpp80)
REVERT: R  318 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7438 (mm)
  outliers start: 40
  outliers final: 22
  residues processed: 158
  average time/residue: 1.4349
  time to fit residues: 239.9348
Evaluate side-chains
  168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  115 VAL
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  318 LEU
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   chunk 98 optimal weight:    0.3980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 304 GLN
E   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9151  Z= 0.174
  Angle     :  0.482   5.121  12420  Z= 0.261
  Chirality :  0.041   0.145   1425
  Planarity :  0.004   0.056   1571
  Dihedral  :  4.362  51.453   1254
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 12.31 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.25), residues: 1144
  helix:  2.60 (0.26), residues: 390
  sheet:  0.38 (0.29), residues: 302
  loop : -0.03 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.012   0.001   TYR R 341 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7989 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7576 (mtm-85)
REVERT: A  208 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7503 (ttm110)
REVERT: A  209 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7823 (ptmm)
REVERT: A  305 CYS cc_start: 0.8234 (m) cc_final: 0.7911 (t)
REVERT: A  312 LYS cc_start: 0.8247 (tppt) cc_final: 0.8045 (mptt)
REVERT: B  134 ARG cc_start: 0.8344 (ptt-90) cc_final: 0.8135 (ptt-90)
REVERT: B  217 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7494 (pmt)
REVERT: C   21 MET cc_start: 0.7631 (mmm) cc_final: 0.6850 (tmm)
REVERT: R  165 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7890 (ttt)
REVERT: R  235 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7844 (tp)
REVERT: R  239 LEU cc_start: 0.7258 (mt) cc_final: 0.7023 (tp)
REVERT: R  252 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5778 (mpp80)
REVERT: R  283 PHE cc_start: 0.7843 (t80) cc_final: 0.6436 (m-10)
  outliers start: 34
  outliers final: 13
  residues processed: 163
  average time/residue: 1.5708
  time to fit residues: 271.0901
Evaluate side-chains
  161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue    4 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 105 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9151  Z= 0.195
  Angle     :  0.493   6.057  12420  Z= 0.265
  Chirality :  0.042   0.145   1425
  Planarity :  0.004   0.056   1571
  Dihedral  :  4.376  51.736   1254
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 12.10 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.25), residues: 1144
  helix:  2.63 (0.26), residues: 389
  sheet:  0.30 (0.29), residues: 304
  loop : -0.05 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 342 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 144
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7983 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7593 (mtm-85)
REVERT: A  197 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8682 (mtmm)
REVERT: A  208 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7533 (ttm110)
REVERT: A  209 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7837 (ptmm)
REVERT: A  305 CYS cc_start: 0.8243 (m) cc_final: 0.7918 (t)
REVERT: B  217 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7483 (pmt)
REVERT: C   21 MET cc_start: 0.7622 (mmm) cc_final: 0.6834 (tmm)
REVERT: R  165 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (ttt)
REVERT: R  235 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (tp)
REVERT: R  239 LEU cc_start: 0.7335 (mt) cc_final: 0.7050 (tp)
REVERT: R  252 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5765 (mpp80)
REVERT: R  283 PHE cc_start: 0.7859 (t80) cc_final: 0.6487 (m-10)
REVERT: R  303 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6953 (mmm160)
  outliers start: 37
  outliers final: 20
  residues processed: 159
  average time/residue: 1.4482
  time to fit residues: 243.7910
Evaluate side-chains
  167 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  318 GLU
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  303 ARG
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0000
   chunk 92 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9151  Z= 0.168
  Angle     :  0.477   5.568  12420  Z= 0.256
  Chirality :  0.041   0.143   1425
  Planarity :  0.003   0.056   1571
  Dihedral  :  4.301  52.007   1254
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 12.20 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.25), residues: 1144
  helix:  2.66 (0.26), residues: 390
  sheet:  0.29 (0.29), residues: 304
  loop : -0.06 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 341 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8256 (ttm170) cc_final: 0.8030 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7454 (mtm110)
REVERT: A  197 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8637 (mtmm)
REVERT: A  208 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7496 (ttm110)
REVERT: A  209 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7820 (ptmm)
REVERT: A  305 CYS cc_start: 0.8201 (m) cc_final: 0.7927 (t)
REVERT: B  134 ARG cc_start: 0.8348 (ptt-90) cc_final: 0.8122 (ptt-90)
REVERT: B  217 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.7464 (pmt)
REVERT: C   21 MET cc_start: 0.7627 (mmm) cc_final: 0.6831 (tmm)
REVERT: R  165 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.8005 (ttt)
REVERT: R  235 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7843 (tp)
REVERT: R  239 LEU cc_start: 0.7307 (mt) cc_final: 0.7043 (tp)
REVERT: R  252 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.5779 (mpp80)
REVERT: R  283 PHE cc_start: 0.7855 (t80) cc_final: 0.6485 (m-10)
REVERT: R  303 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6823 (mmm160)
  outliers start: 33
  outliers final: 18
  residues processed: 153
  average time/residue: 1.5149
  time to fit residues: 244.8007
Evaluate side-chains
  162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  303 ARG
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 69 optimal weight:    0.5980
   chunk 74 optimal weight:    6.9990
   chunk 53 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9151  Z= 0.185
  Angle     :  0.486   5.804  12420  Z= 0.261
  Chirality :  0.041   0.143   1425
  Planarity :  0.003   0.055   1571
  Dihedral  :  4.325  52.128   1254
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 12.93 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1144
  helix:  2.67 (0.26), residues: 390
  sheet:  0.20 (0.28), residues: 307
  loop : -0.04 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 342 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8252 (ttm170) cc_final: 0.8028 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7474 (mtm110)
REVERT: A  208 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7487 (ttm110)
REVERT: A  209 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7872 (ptmm)
REVERT: A  305 CYS cc_start: 0.8201 (m) cc_final: 0.7890 (t)
REVERT: B  134 ARG cc_start: 0.8353 (ptt-90) cc_final: 0.8127 (ptt-90)
REVERT: B  217 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7444 (pmt)
REVERT: C   21 MET cc_start: 0.7626 (mmm) cc_final: 0.6823 (tmm)
REVERT: R  165 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7999 (ttt)
REVERT: R  235 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7848 (tp)
REVERT: R  239 LEU cc_start: 0.7295 (mt) cc_final: 0.7032 (tp)
REVERT: R  252 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.5777 (mpp80)
REVERT: R  283 PHE cc_start: 0.7860 (t80) cc_final: 0.6485 (m-10)
REVERT: R  303 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6860 (mmm160)
  outliers start: 31
  outliers final: 19
  residues processed: 150
  average time/residue: 1.5370
  time to fit residues: 243.4082
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  303 ARG
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0670
   chunk 44 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9151  Z= 0.198
  Angle     :  0.497   6.155  12420  Z= 0.267
  Chirality :  0.042   0.144   1425
  Planarity :  0.004   0.055   1571
  Dihedral  :  4.372  52.206   1254
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.34 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1144
  helix:  2.65 (0.26), residues: 390
  sheet:  0.19 (0.28), residues: 307
  loop : -0.05 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 248 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.014   0.001   TYR R 342 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8245 (ttm170) cc_final: 0.8019 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7474 (mtm110)
REVERT: A  208 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7482 (ttm110)
REVERT: A  209 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7830 (ptmm)
REVERT: A  305 CYS cc_start: 0.8203 (m) cc_final: 0.7887 (t)
REVERT: B  217 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7427 (pmt)
REVERT: C   21 MET cc_start: 0.7625 (mmm) cc_final: 0.6821 (tmm)
REVERT: R  165 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.8017 (ttt)
REVERT: R  235 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7820 (tp)
REVERT: R  239 LEU cc_start: 0.7303 (mt) cc_final: 0.7042 (tp)
REVERT: R  252 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.5771 (mpp80)
REVERT: R  283 PHE cc_start: 0.7865 (t80) cc_final: 0.6486 (m-10)
REVERT: R  303 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6867 (mmm160)
  outliers start: 30
  outliers final: 20
  residues processed: 150
  average time/residue: 1.5129
  time to fit residues: 239.8574
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 133
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  165 MET
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  303 ARG
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 112 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0980
   chunk 69 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9151  Z= 0.197
  Angle     :  0.499   6.895  12420  Z= 0.267
  Chirality :  0.042   0.143   1425
  Planarity :  0.004   0.055   1571
  Dihedral  :  4.371  52.227   1254
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 13.65 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.25), residues: 1144
  helix:  2.66 (0.26), residues: 390
  sheet:  0.19 (0.28), residues: 307
  loop : -0.08 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 248 
 HIS   0.005   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 342 
 ARG   0.002   0.000   ARG B 251 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8241 (ttm170) cc_final: 0.8016 (ttp-110)
REVERT: A   24 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7475 (mtm110)
REVERT: A  197 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8639 (mtmm)
REVERT: A  208 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7510 (ttm110)
REVERT: A  209 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7879 (ptmm)
REVERT: A  305 CYS cc_start: 0.8195 (m) cc_final: 0.7911 (t)
REVERT: B  217 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7433 (pmt)
REVERT: C   21 MET cc_start: 0.7620 (mmm) cc_final: 0.6806 (tmm)
REVERT: R  235 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7852 (tp)
REVERT: R  239 LEU cc_start: 0.7307 (mt) cc_final: 0.7047 (tp)
REVERT: R  252 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.5821 (mpp80)
REVERT: R  283 PHE cc_start: 0.7867 (t80) cc_final: 0.6487 (m-10)
REVERT: R  303 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6962 (mmm160)
  outliers start: 27
  outliers final: 19
  residues processed: 149
  average time/residue: 1.5122
  time to fit residues: 237.8898
Evaluate side-chains
  159 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain R residue  184 MET
Chi-restraints excluded: chain R residue  185 CYS
Chi-restraints excluded: chain R residue  192 ASP
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  252 ARG
Chi-restraints excluded: chain R residue  280 TYR
Chi-restraints excluded: chain R residue  303 ARG
Chi-restraints excluded: chain R residue  304 MET
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain R residue  336 VAL
Chi-restraints excluded: chain R residue  386 THR
Chi-restraints excluded: chain L residue    8 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.171481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.136633 restraints weight = 9074.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 1.69
r_work: 0.3290 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9151  Z= 0.279
  Angle     :  0.549   7.326  12420  Z= 0.293
  Chirality :  0.043   0.148   1425
  Planarity :  0.004   0.056   1571
  Dihedral  :  4.577  52.116   1254
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.55 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1144
  helix:  2.51 (0.26), residues: 391
  sheet:  0.15 (0.28), residues: 307
  loop : -0.15 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 248 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.021   0.002   PHE B 151 
 TYR   0.017   0.002   TYR E 103 
 ARG   0.002   0.000   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4084.10 seconds
wall clock time: 73 minutes 46.89 seconds (4426.89 seconds total)