Starting phenix.real_space_refine
on Thu Mar 13 03:43:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2025/7vdl_31922.cif"
  }
  resolution = 3.22
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      64      5.16       5
     C    5513      2.51       5
     N    1440      2.21       5
     O    1581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8598
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1727
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1727
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2590
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 415
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1757
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 2036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2036
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
    Chain: "L"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 45
          Classifications: {'peptide': 5}
          Link IDs: {'TRANS': 4}
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.67, per 1000 atoms: 0.66
  Number of scatterers: 8598
  At special positions: 0
  Unit cell: (117.52, 104, 106.08, 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      64     16.00
     O    1581      8.00
     N    1440      7.00
     C    5513      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.07
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " 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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.7% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.577A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.586A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.055A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 242 through 255
      removed outlier: 3.734A  pdb=" N   ASN A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 4.097A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 5.520A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   SER A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.724A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 309
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.622A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.664A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 3.663A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.135A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'R' and resid 31 through 58
    Processing helix  chain 'R' and resid 62 through 94
      removed outlier: 3.601A  pdb=" N   VAL R  66 " --> pdb=" O   ASN R  62 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   TYR R  67 " --> pdb=" O   ALA R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 104 through 133
      removed outlier: 4.018A  pdb=" N   VAL R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 169
    Processing helix  chain 'R' and resid 176 through 213
      removed outlier: 4.007A  pdb=" N   PHE R 183 " --> pdb=" O   TRP R 179 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 235
    Processing helix  chain 'R' and resid 236 through 245
      removed outlier: 4.594A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 246 through 249
    Processing helix  chain 'R' and resid 254 through 280
      removed outlier: 4.342A  pdb=" N   CYS R 258 " --> pdb=" O   ASP R 254 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   HIS R 259 " --> pdb=" O   VAL R 255 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   HIS R 261 " --> pdb=" O   PHE R 257 " (cutoff:3.500A)
      Proline residue:  R 262  - end of helix
      removed outlier: 3.540A  pdb=" N   VAL R 265 " --> pdb=" O   HIS R 261 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 280 through 285
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38
      removed outlier: 3.651A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 226
      removed outlier: 5.518A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.555A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.027A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.759A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.584A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.546A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.712A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277
      removed outlier: 4.002A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.547A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.677A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.677A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 116 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 129 through 130
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.552A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1230 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: 2.70

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2693
        1.34 -     1.47: 2328
        1.47 -     1.60: 3678
        1.60 -     1.74: 1
        1.74 -     1.87: 88
  Bond restraints: 8788
  Sorted by residual:
  bond pdb=" C17 CLR R 401 "
       pdb=" C20 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.647 -0.112 2.00e-02 2.50e+03 3.14e+01
  bond pdb=" CA  ARG R  61 "
       pdb=" C   ARG R  61 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.18e-02 7.18e+03 1.34e+01
  bond pdb=" C   HIS R 261 "
       pdb=" N   PRO R 262 "
    ideal  model  delta    sigma   weight residual
    1.336  1.369 -0.033 1.20e-02 6.94e+03 7.45e+00
  bond pdb=" CA  ARG B  52 "
       pdb=" CB  ARG B  52 "
    ideal  model  delta    sigma   weight residual
    1.527  1.589 -0.061 2.48e-02 1.63e+03 6.14e+00
  bond pdb=" CA  PHE R 281 "
       pdb=" C   PHE R 281 "
    ideal  model  delta    sigma   weight residual
    1.524  1.493  0.031 1.29e-02 6.01e+03 5.74e+00
  ... (remaining 8783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 11568
        2.99 -     5.99: 288
        5.99 -     8.98: 42
        8.98 -    11.97: 11
       11.97 -    14.97: 4
  Bond angle restraints: 11913
  Sorted by residual:
  angle pdb=" N   TYR R 279 "
        pdb=" CA  TYR R 279 "
        pdb=" C   TYR R 279 "
      ideal   model   delta    sigma   weight residual
     111.36  119.24   -7.88 1.09e+00 8.42e-01 5.23e+01
  angle pdb=" N   ILE R 278 "
        pdb=" CA  ILE R 278 "
        pdb=" C   ILE R 278 "
      ideal   model   delta    sigma   weight residual
     110.42  117.13   -6.71 9.60e-01 1.09e+00 4.88e+01
  angle pdb=" N   ARG R  61 "
        pdb=" CA  ARG R  61 "
        pdb=" C   ARG R  61 "
      ideal   model   delta    sigma   weight residual
     109.95  119.88   -9.93 1.59e+00 3.96e-01 3.90e+01
  angle pdb=" N   PHE R 281 "
        pdb=" CA  PHE R 281 "
        pdb=" C   PHE R 281 "
      ideal   model   delta    sigma   weight residual
     111.36  117.45   -6.09 1.09e+00 8.42e-01 3.12e+01
  angle pdb=" CA  CYS B 149 "
        pdb=" CB  CYS B 149 "
        pdb=" SG  CYS B 149 "
      ideal   model   delta    sigma   weight residual
     114.40  127.06  -12.66 2.30e+00 1.89e-01 3.03e+01
  ... (remaining 11908 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4717
       17.97 -    35.93: 412
       35.93 -    53.90: 66
       53.90 -    71.86: 10
       71.86 -    89.83: 5
  Dihedral angle restraints: 5210
    sinusoidal: 2038
      harmonic: 3172
  Sorted by residual:
  dihedral pdb=" CA  THR A 295 "
           pdb=" C   THR A 295 "
           pdb=" N   TYR A 296 "
           pdb=" CA  TYR A 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.87   26.13     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" N   ASN L  24 "
           pdb=" C   ASN L  24 "
           pdb=" CA  ASN L  24 "
           pdb=" CB  ASN L  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.03  -12.23     0      2.50e+00 1.60e-01 2.39e+01
  dihedral pdb=" CA  LEU B 261 "
           pdb=" C   LEU B 261 "
           pdb=" N   MET B 262 "
           pdb=" CA  MET B 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.84  -24.16     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 5207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1219
       0.104 -    0.208: 121
       0.208 -    0.311: 8
       0.311 -    0.415: 5
       0.415 -    0.519: 5
  Chirality restraints: 1358
  Sorted by residual:
  chirality pdb=" CA  ASN L  24 "
            pdb=" N   ASN L  24 "
            pdb=" C   ASN L  24 "
            pdb=" CB  ASN L  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.73e+00
  chirality pdb=" CB  ILE R  32 "
            pdb=" CA  ILE R  32 "
            pdb=" CG1 ILE R  32 "
            pdb=" CG2 ILE R  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.18    0.46 2.00e-01 2.50e+01 5.30e+00
  chirality pdb=" CA  ARG R  61 "
            pdb=" N   ARG R  61 "
            pdb=" C   ARG R  61 "
            pdb=" CB  ARG R  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.27e+00
  ... (remaining 1355 not shown)

  Planarity restraints: 1490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S 103 "   -0.006 2.00e-02 2.50e+03   2.31e-02 1.07e+01
        pdb=" CG  TYR S 103 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR S 103 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR S 103 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR S 103 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR S 103 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR S 103 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR S 103 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET S 180 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   MET S 180 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   MET S 180 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER S 181 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.21e+00
        pdb=" N   PRO C  53 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1487 not shown)

  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 24
        2.37 -     3.01: 4227
        3.01 -     3.64: 13199
        3.64 -     4.27: 20292
        4.27 -     4.90: 34051
  Nonbonded interactions: 71793
  Sorted by model distance:
  nonbonded pdb=" O   PHE R  50 "
            pdb=" CD1 LEU R  54 "
     model   vdw
     1.743 3.460
  nonbonded pdb=" CD1 LEU R 120 "
            pdb=" OH  TYR R 279 "
     model   vdw
     2.062 3.460
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   SER S  30 "
            pdb=" OG  SER S  53 "
     model   vdw
     2.237 3.040
  ... (remaining 71788 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:             0.430
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.640
  Find NCS groups from input model:        0.100
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
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      :  0.008   0.112   8788  Z= 0.511
  Angle     :  1.158  14.967  11913  Z= 0.619
  Chirality :  0.069   0.519   1358
  Planarity :  0.007   0.076   1490
  Dihedral  : 13.815  89.831   3155
  Min Nonbonded Distance : 1.743

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.18 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -1.82 (0.24), residues: 1082
  helix: -1.14 (0.23), residues: 380
  sheet: -0.84 (0.31), residues: 277
  loop : -1.29 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 297 
 HIS   0.004   0.002   HIS A 322 
 PHE   0.043   0.004   PHE R 257 
 TYR   0.049   0.004   TYR S 103 
 ARG   0.020   0.001   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 ASP cc_start: 0.7046 (t0) cc_final: 0.6772 (t0)
REVERT: A  277 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7317 (tptt)
REVERT: A  304 GLN cc_start: 0.8266 (tm130) cc_final: 0.8018 (tm-30)
REVERT: B  211 TRP cc_start: 0.8839 (m100) cc_final: 0.8396 (m100)
REVERT: S  218 MET cc_start: 0.9086 (ttp) cc_final: 0.8818 (ttp)
REVERT: R  158 LEU cc_start: 0.7833 (tp) cc_final: 0.7311 (tt)
REVERT: R  163 LEU cc_start: 0.7570 (tt) cc_final: 0.7256 (tp)
REVERT: R  183 PHE cc_start: 0.4481 (m-80) cc_final: 0.4103 (m-80)
REVERT: L   22 CYS cc_start: 0.4938 (p) cc_final: 0.4218 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2300
  time to fit residues: 67.1052
Evaluate side-chains
  198 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 97 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:
B 220 GLN
S   3 GLN
S 182 ASN
L  24 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.184757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148574 restraints weight = 9936.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.20
r_work: 0.3493 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8788  Z= 0.198
  Angle     :  0.673  14.229  11913  Z= 0.337
  Chirality :  0.045   0.261   1358
  Planarity :  0.004   0.053   1490
  Dihedral  :  6.620  59.331   1245
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  8.56 %
    Favored  : 90.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.81 (0.25), residues: 1082
  helix:  0.27 (0.26), residues: 383
  sheet: -0.64 (0.31), residues: 268
  loop : -1.06 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 188 
 PHE   0.030   0.002   PHE R  50 
 TYR   0.025   0.002   TYR R 279 
 ARG   0.005   0.000   ARG B 283 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 221
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 ASP cc_start: 0.7954 (t0) cc_final: 0.7736 (t0)
REVERT: B   13 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7236 (pt0)
REVERT: S   19 LYS cc_start: 0.7612 (tttp) cc_final: 0.7012 (ttpt)
REVERT: S   65 LYS cc_start: 0.8149 (tptt) cc_final: 0.7590 (mmtt)
REVERT: S  206 ARG cc_start: 0.6933 (ptt-90) cc_final: 0.6403 (mmp80)
REVERT: R   35 PHE cc_start: 0.6935 (m-80) cc_final: 0.6596 (m-80)
REVERT: R   61 ARG cc_start: 0.5585 (mtm-85) cc_final: 0.5164 (mtm-85)
REVERT: R  158 LEU cc_start: 0.7896 (tp) cc_final: 0.7380 (tt)
REVERT: R  180 CYS cc_start: 0.7432 (t) cc_final: 0.7125 (t)
REVERT: R  193 PHE cc_start: 0.8169 (t80) cc_final: 0.7881 (t80)
REVERT: R  208 ARG cc_start: 0.7633 (tpt90) cc_final: 0.7423 (tpt90)
REVERT: R  248 TRP cc_start: 0.7814 (m100) cc_final: 0.7601 (m100)
  outliers start: 13
  outliers final: 7
  residues processed: 225
  average time/residue: 0.2331
  time to fit residues: 69.8299
Evaluate side-chains
  196 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 189
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain L residue   24 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
S   3 GLN
S 167 GLN
L  24 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.182518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.145968 restraints weight = 10241.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.28
r_work: 0.3456 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8788  Z= 0.233
  Angle     :  0.657  14.167  11913  Z= 0.328
  Chirality :  0.044   0.278   1358
  Planarity :  0.004   0.045   1490
  Dihedral  :  6.337  59.405   1245
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.73 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.34 (0.25), residues: 1082
  helix:  0.80 (0.26), residues: 391
  sheet: -0.47 (0.31), residues: 277
  loop : -0.93 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.021   0.001   PHE R  50 
 TYR   0.037   0.002   TYR A 296 
 ARG   0.004   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.7899 (pm20) cc_final: 0.7660 (pm20)
REVERT: A  312 LYS cc_start: 0.8324 (mmtp) cc_final: 0.7750 (mmmt)
REVERT: B   13 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7178 (pt0)
REVERT: S   65 LYS cc_start: 0.8132 (tptt) cc_final: 0.7879 (tptt)
REVERT: R   35 PHE cc_start: 0.6804 (m-80) cc_final: 0.6320 (m-80)
REVERT: R   59 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6543 (mtm)
REVERT: R  158 LEU cc_start: 0.7887 (tp) cc_final: 0.7440 (tt)
REVERT: R  180 CYS cc_start: 0.7466 (t) cc_final: 0.7088 (t)
REVERT: R  183 PHE cc_start: 0.5844 (m-80) cc_final: 0.5448 (m-80)
REVERT: R  193 PHE cc_start: 0.8188 (t80) cc_final: 0.7849 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 206
  average time/residue: 0.2362
  time to fit residues: 65.0703
Evaluate side-chains
  205 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 194
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  218 LEU
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain L residue   22 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 29 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0470
   chunk 15 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
B 220 GLN
S   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.186437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150268 restraints weight = 9987.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.27
r_work: 0.3513 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8788  Z= 0.156
  Angle     :  0.591  11.133  11913  Z= 0.298
  Chirality :  0.042   0.267   1358
  Planarity :  0.003   0.038   1490
  Dihedral  :  6.047  59.447   1245
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 14.87 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -0.03 (0.26), residues: 1082
  helix:  1.26 (0.27), residues: 391
  sheet: -0.36 (0.31), residues: 270
  loop : -0.92 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.014   0.001   PHE R  76 
 TYR   0.039   0.002   TYR A 296 
 ARG   0.004   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8095 (tt0) cc_final: 0.7861 (tt0)
REVERT: A  276 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6162 (tp30)
REVERT: A  289 GLU cc_start: 0.7921 (pm20) cc_final: 0.7582 (pm20)
REVERT: B   13 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7275 (pt0)
REVERT: B   23 LYS cc_start: 0.8329 (tppt) cc_final: 0.8111 (tppt)
REVERT: S   19 LYS cc_start: 0.7719 (tttp) cc_final: 0.7129 (ttpt)
REVERT: S   65 LYS cc_start: 0.8161 (tptt) cc_final: 0.7574 (mmtt)
REVERT: S  206 ARG cc_start: 0.6890 (ptt-90) cc_final: 0.6298 (mmp80)
REVERT: R   35 PHE cc_start: 0.6961 (m-80) cc_final: 0.6454 (m-80)
REVERT: R   59 MET cc_start: 0.6899 (mtp) cc_final: 0.6606 (mtm)
REVERT: R  158 LEU cc_start: 0.7882 (tp) cc_final: 0.7485 (tt)
REVERT: R  183 PHE cc_start: 0.5632 (m-80) cc_final: 0.5268 (m-80)
REVERT: R  193 PHE cc_start: 0.8083 (t80) cc_final: 0.7824 (t80)
REVERT: R  278 ILE cc_start: 0.8175 (mt) cc_final: 0.7942 (mt)
  outliers start: 18
  outliers final: 11
  residues processed: 224
  average time/residue: 0.2254
  time to fit residues: 67.7014
Evaluate side-chains
  214 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 85 optimal weight:    0.1980
   chunk 51 optimal weight:    4.9990
   chunk 89 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 7 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
S   3 GLN
R  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.186044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.150208 restraints weight = 9911.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.26
r_work: 0.3510 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8788  Z= 0.166
  Angle     :  0.583  14.793  11913  Z= 0.294
  Chirality :  0.042   0.264   1358
  Planarity :  0.003   0.035   1490
  Dihedral  :  5.961  59.808   1245
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.33 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.24 (0.26), residues: 1082
  helix:  1.49 (0.27), residues: 395
  sheet: -0.09 (0.32), residues: 261
  loop : -0.89 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.013   0.001   PHE R  76 
 TYR   0.037   0.002   TYR A 296 
 ARG   0.003   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7213 (tt0)
REVERT: A  193 ASP cc_start: 0.7989 (t0) cc_final: 0.7673 (t0)
REVERT: A  247 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8239 (ttt)
REVERT: B   13 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7406 (pt0)
REVERT: B   23 LYS cc_start: 0.8313 (tppt) cc_final: 0.8086 (tppt)
REVERT: S   19 LYS cc_start: 0.7800 (tttp) cc_final: 0.7248 (ttpt)
REVERT: S   65 LYS cc_start: 0.8102 (tptt) cc_final: 0.7505 (mmtt)
REVERT: S  206 ARG cc_start: 0.6890 (ptt-90) cc_final: 0.6316 (mmp80)
REVERT: R   35 PHE cc_start: 0.7033 (m-80) cc_final: 0.6481 (m-80)
REVERT: R   59 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6620 (mtm)
REVERT: R   67 TYR cc_start: 0.7953 (m-80) cc_final: 0.7503 (m-80)
REVERT: R  140 ARG cc_start: 0.8409 (mtm110) cc_final: 0.8030 (mtm110)
REVERT: R  183 PHE cc_start: 0.5702 (m-80) cc_final: 0.5154 (m-80)
REVERT: R  193 PHE cc_start: 0.8105 (t80) cc_final: 0.7826 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 215
  average time/residue: 0.2350
  time to fit residues: 67.0151
Evaluate side-chains
  205 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 193
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 88 optimal weight:    9.9990
   chunk 61 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0970
   chunk 90 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
R  48 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.186533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.150280 restraints weight = 9882.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.26
r_work: 0.3509 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8788  Z= 0.171
  Angle     :  0.589  13.102  11913  Z= 0.295
  Chirality :  0.042   0.259   1358
  Planarity :  0.003   0.033   1490
  Dihedral  :  5.853  58.631   1245
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.07 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.40 (0.26), residues: 1082
  helix:  1.71 (0.27), residues: 389
  sheet: -0.06 (0.32), residues: 263
  loop : -0.82 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.013   0.001   PHE R  76 
 TYR   0.040   0.002   TYR A 296 
 ARG   0.003   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7202 (tt0)
REVERT: A  188 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6698 (m-70)
REVERT: A  193 ASP cc_start: 0.7926 (t0) cc_final: 0.7622 (t0)
REVERT: B   13 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7458 (pt0)
REVERT: B   23 LYS cc_start: 0.8332 (tppt) cc_final: 0.8107 (tppt)
REVERT: S   19 LYS cc_start: 0.7750 (tttp) cc_final: 0.7274 (ttpt)
REVERT: S   73 ASP cc_start: 0.7359 (p0) cc_final: 0.6621 (t70)
REVERT: S  206 ARG cc_start: 0.6835 (ptt-90) cc_final: 0.6367 (mmp80)
REVERT: R   35 PHE cc_start: 0.7074 (m-80) cc_final: 0.6471 (m-80)
REVERT: R   59 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6605 (mtm)
REVERT: R  101 PHE cc_start: 0.5813 (t80) cc_final: 0.5546 (t80)
REVERT: R  140 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8034 (mtm110)
REVERT: R  183 PHE cc_start: 0.5599 (m-80) cc_final: 0.5062 (m-80)
REVERT: R  193 PHE cc_start: 0.8133 (t80) cc_final: 0.7858 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 216
  average time/residue: 0.2408
  time to fit residues: 68.9592
Evaluate side-chains
  217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  230 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
R  48 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.185919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.149930 restraints weight = 9995.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.26
r_work: 0.3505 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8788  Z= 0.174
  Angle     :  0.596  12.374  11913  Z= 0.297
  Chirality :  0.042   0.252   1358
  Planarity :  0.003   0.032   1490
  Dihedral  :  5.759  58.922   1245
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.93 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.48 (0.26), residues: 1082
  helix:  1.76 (0.27), residues: 389
  sheet: -0.10 (0.31), residues: 268
  loop : -0.70 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.014   0.001   PHE R  76 
 TYR   0.039   0.002   TYR A 296 
 ARG   0.003   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8226 (mt-10) cc_final: 0.8007 (mt-10)
REVERT: A  188 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6682 (m-70)
REVERT: A  193 ASP cc_start: 0.7873 (t0) cc_final: 0.7564 (t0)
REVERT: B   13 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7467 (pt0)
REVERT: B   23 LYS cc_start: 0.8268 (tppt) cc_final: 0.8017 (tppt)
REVERT: B  119 ASN cc_start: 0.9068 (m-40) cc_final: 0.8810 (m-40)
REVERT: B  234 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8057 (m-80)
REVERT: S   19 LYS cc_start: 0.7850 (tttp) cc_final: 0.7472 (ttpt)
REVERT: S   73 ASP cc_start: 0.7379 (p0) cc_final: 0.6588 (t70)
REVERT: S   80 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.5694 (p90)
REVERT: S  206 ARG cc_start: 0.6864 (ptt-90) cc_final: 0.6325 (mmp80)
REVERT: R   35 PHE cc_start: 0.7250 (m-80) cc_final: 0.6635 (m-80)
REVERT: R   59 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6398 (mtm)
REVERT: R  101 PHE cc_start: 0.5778 (t80) cc_final: 0.5516 (t80)
REVERT: R  140 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8024 (mtm110)
REVERT: R  193 PHE cc_start: 0.8124 (t80) cc_final: 0.7861 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 217
  average time/residue: 0.2297
  time to fit residues: 66.2868
Evaluate side-chains
  218 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  248 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 84 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
S 174 GLN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.186093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.149362 restraints weight = 10095.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.28
r_work: 0.3500 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8788  Z= 0.180
  Angle     :  0.619  15.854  11913  Z= 0.302
  Chirality :  0.042   0.244   1358
  Planarity :  0.003   0.031   1490
  Dihedral  :  5.637  55.786   1245
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.47 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.52 (0.26), residues: 1082
  helix:  1.74 (0.27), residues: 389
  sheet: -0.02 (0.32), residues: 266
  loop : -0.67 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R 167 
 TYR   0.041   0.002   TYR A 296 
 ARG   0.003   0.000   ARG R  61 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7992 (mt-10)
REVERT: A  188 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6696 (m-70)
REVERT: A  193 ASP cc_start: 0.7821 (t0) cc_final: 0.7522 (t0)
REVERT: B   13 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7457 (pt0)
REVERT: B   23 LYS cc_start: 0.8263 (tppt) cc_final: 0.8018 (tppt)
REVERT: B  119 ASN cc_start: 0.9043 (m-40) cc_final: 0.8737 (m-40)
REVERT: B  234 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8112 (m-80)
REVERT: S   19 LYS cc_start: 0.7823 (tttp) cc_final: 0.7446 (ttpt)
REVERT: S   23 SER cc_start: 0.8361 (p) cc_final: 0.7865 (m)
REVERT: S   73 ASP cc_start: 0.7432 (p0) cc_final: 0.6683 (t70)
REVERT: S   80 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.5645 (p90)
REVERT: S  206 ARG cc_start: 0.6895 (ptt-90) cc_final: 0.6321 (mmp80)
REVERT: R   35 PHE cc_start: 0.7258 (m-80) cc_final: 0.6734 (m-80)
REVERT: R   59 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6427 (mtm)
REVERT: R  101 PHE cc_start: 0.5729 (t80) cc_final: 0.5517 (t80)
REVERT: R  104 PHE cc_start: 0.6241 (t80) cc_final: 0.5875 (t80)
REVERT: R  140 ARG cc_start: 0.8398 (mtm110) cc_final: 0.8040 (mtm110)
REVERT: R  158 LEU cc_start: 0.7730 (tp) cc_final: 0.7435 (tt)
REVERT: R  167 PHE cc_start: 0.6903 (m-80) cc_final: 0.6566 (m-80)
REVERT: R  193 PHE cc_start: 0.8125 (t80) cc_final: 0.7855 (t80)
REVERT: R  278 ILE cc_start: 0.8090 (mt) cc_final: 0.7874 (mt)
  outliers start: 22
  outliers final: 16
  residues processed: 211
  average time/residue: 0.2379
  time to fit residues: 66.6041
Evaluate side-chains
  224 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  248 TRP
Chi-restraints excluded: chain R residue  268 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 95 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
S   3 GLN
S 174 GLN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.182996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.145865 restraints weight = 10060.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.25
r_work: 0.3467 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8788  Z= 0.255
  Angle     :  0.660  15.090  11913  Z= 0.324
  Chirality :  0.044   0.252   1358
  Planarity :  0.003   0.032   1490
  Dihedral  :  5.852  57.459   1245
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.11 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.39 (0.26), residues: 1082
  helix:  1.60 (0.27), residues: 388
  sheet: -0.20 (0.32), residues: 269
  loop : -0.60 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.015   0.001   PHE R 167 
 TYR   0.038   0.002   TYR A 296 
 ARG   0.003   0.000   ARG S  87 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 206
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7163 (tt0)
REVERT: A  188 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6777 (m-70)
REVERT: A  193 ASP cc_start: 0.7804 (t0) cc_final: 0.7529 (t0)
REVERT: A  312 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7851 (mmmt)
REVERT: B   13 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7402 (pt0)
REVERT: B   23 LYS cc_start: 0.8271 (tppt) cc_final: 0.7981 (tppt)
REVERT: B  234 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8144 (m-80)
REVERT: S   73 ASP cc_start: 0.7528 (p0) cc_final: 0.6752 (t70)
REVERT: S   80 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.5763 (p90)
REVERT: S  206 ARG cc_start: 0.6944 (ptt-90) cc_final: 0.6344 (mmp80)
REVERT: R   35 PHE cc_start: 0.7237 (m-80) cc_final: 0.6720 (m-80)
REVERT: R   59 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6447 (mtm)
REVERT: R   61 ARG cc_start: 0.5610 (ptp-110) cc_final: 0.4712 (ptt180)
REVERT: R  104 PHE cc_start: 0.6237 (t80) cc_final: 0.5875 (t80)
REVERT: R  158 LEU cc_start: 0.7797 (tp) cc_final: 0.7475 (tt)
REVERT: R  167 PHE cc_start: 0.6929 (m-80) cc_final: 0.6104 (m-10)
REVERT: R  278 ILE cc_start: 0.8228 (mt) cc_final: 0.8023 (mt)
  outliers start: 26
  outliers final: 17
  residues processed: 218
  average time/residue: 0.2336
  time to fit residues: 67.7326
Evaluate side-chains
  223 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   59 MET
Chi-restraints excluded: chain R residue   83 ILE
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  268 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 104 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
S 174 GLN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.184288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.147286 restraints weight = 10040.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.25
r_work: 0.3483 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8788  Z= 0.207
  Angle     :  0.649  16.379  11913  Z= 0.317
  Chirality :  0.043   0.244   1358
  Planarity :  0.003   0.031   1490
  Dihedral  :  5.739  55.719   1245
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 20.86 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  0.42 (0.26), residues: 1082
  helix:  1.63 (0.27), residues: 389
  sheet: -0.04 (0.32), residues: 261
  loop : -0.70 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 248 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.014   0.001   PHE R  76 
 TYR   0.041   0.002   TYR A 296 
 ARG   0.002   0.000   ARG B 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 204
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7175 (tt0)
REVERT: A  188 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6739 (m-70)
REVERT: A  193 ASP cc_start: 0.7811 (t0) cc_final: 0.7522 (t0)
REVERT: A  271 LYS cc_start: 0.7673 (pttt) cc_final: 0.7249 (tttm)
REVERT: A  312 LYS cc_start: 0.8402 (mmtp) cc_final: 0.7833 (mmmt)
REVERT: B   13 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7464 (pt0)
REVERT: B   23 LYS cc_start: 0.8273 (tppt) cc_final: 0.7981 (tppt)
REVERT: B  234 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8116 (m-80)
REVERT: B  297 TRP cc_start: 0.8624 (m100) cc_final: 0.8398 (m100)
REVERT: S   19 LYS cc_start: 0.7733 (tttp) cc_final: 0.7366 (ttpt)
REVERT: S   73 ASP cc_start: 0.7536 (p0) cc_final: 0.6789 (t70)
REVERT: S   80 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.5664 (p90)
REVERT: S   83 MET cc_start: 0.7814 (ptp) cc_final: 0.7495 (ptp)
REVERT: S  206 ARG cc_start: 0.6991 (ptt-90) cc_final: 0.6436 (mmp80)
REVERT: R   35 PHE cc_start: 0.7314 (m-80) cc_final: 0.6785 (m-80)
REVERT: R   61 ARG cc_start: 0.5699 (ptp-110) cc_final: 0.4682 (ptt180)
REVERT: R  104 PHE cc_start: 0.6238 (t80) cc_final: 0.5850 (t80)
REVERT: R  140 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7979 (mtm110)
REVERT: R  158 LEU cc_start: 0.7789 (tp) cc_final: 0.7493 (tt)
REVERT: R  167 PHE cc_start: 0.6872 (m-80) cc_final: 0.6055 (m-10)
REVERT: R  278 ILE cc_start: 0.8185 (mt) cc_final: 0.7973 (mt)
  outliers start: 21
  outliers final: 16
  residues processed: 214
  average time/residue: 0.2575
  time to fit residues: 73.2550
Evaluate side-chains
  217 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 HIS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  160 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain S residue    7 SER
Chi-restraints excluded: chain S residue   30 SER
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue  132 LEU
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  223 LEU
Chi-restraints excluded: chain R residue  268 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0470
   chunk 80 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
S   3 GLN
S 174 GLN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.185119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.148709 restraints weight = 10057.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.25
r_work: 0.3509 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8788  Z= 0.176
  Angle     :  0.641  16.254  11913  Z= 0.311
  Chirality :  0.043   0.223   1358
  Planarity :  0.003   0.030   1490
  Dihedral  :  5.435  49.435   1245
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.96 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1082
  helix:  1.70 (0.27), residues: 390
  sheet:  0.09 (0.33), residues: 255
  loop : -0.72 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.035   0.001   PHE R 193 
 TYR   0.041   0.002   TYR A 296 
 ARG   0.002   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5174.11 seconds
wall clock time: 89 minutes 23.09 seconds (5363.09 seconds total)