Starting phenix.real_space_refine
on Mon Jun  9 15:42:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w0p_32247/06_2025/7w0p_32247.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2057 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     C    5788      2.51       5
     N    1541      2.21       5
     O    1694      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9091
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1813
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
    Chain: "R"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2337
          Classifications: {'peptide': 292}
          Link IDs: {'PTRANS': 11, 'TRANS': 280}
    Chain: "S"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 128
          Classifications: {'peptide': 15}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 11}
  Time building chain proxies: 6.10, per 1000 atoms: 0.67
  Number of scatterers: 9091
  At special positions: 0
  Unit cell: (90.48, 118.56, 132.08, 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      68     16.00
     O    1694      8.00
     N    1541      7.00
     C    5788      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " 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: 2.60
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2166

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 13 sheets defined
      37.9% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.553A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.714A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 207 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.049A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 39 through 55
      removed outlier: 3.597A  pdb=" N   ASN C  55 " --> pdb=" O   LYS C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 76
    Processing helix  chain 'R' and resid 29 through 55
      removed outlier: 4.245A  pdb=" N   ALA R  33 " --> pdb=" O   ALA R  29 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR R  52 " --> pdb=" O   LEU R  48 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 80
    Processing helix  chain 'R' and resid 81 through 86
      removed outlier: 3.648A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 92
    Processing helix  chain 'R' and resid 98 through 133
      removed outlier: 3.736A  pdb=" N   CYS R 102 " --> pdb=" O   GLY R  98 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR R 107 " --> pdb=" O   LYS R 103 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   ARG R 133 " --> pdb=" O   LEU R 129 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 147
      removed outlier: 3.936A  pdb=" N   GLY R 146 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ALA R 147 " --> pdb=" O   ARG R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 147 through 162
    Processing helix  chain 'R' and resid 163 through 165
      No H-bonds generated for 'chain 'R' and resid 163 through 165'
    Processing helix  chain 'R' and resid 190 through 233
      removed outlier: 4.159A  pdb=" N   TRP R 195 " --> pdb=" O   VAL R 191 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY R 209 " --> pdb=" O   SER R 205 " (cutoff:3.500A)
      Proline residue:  R 213  - end of helix
      removed outlier: 4.276A  pdb=" N   ARG R 233 " --> pdb=" O   ALA R 229 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 236 through 274
      removed outlier: 4.230A  pdb=" N   ARG R 241 " --> pdb=" O   ILE R 237 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LYS R 242 " --> pdb=" O   GLU R 238 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL R 254 " --> pdb=" O   ILE R 250 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
    Processing helix  chain 'R' and resid 280 through 310
      removed outlier: 3.561A  pdb=" N   ASP R 284 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE R 286 " --> pdb=" O   ASP R 282 " (cutoff:3.500A)
      Proline residue:  R 292  - end of helix
      removed outlier: 3.893A  pdb=" N   CYS R 296 " --> pdb=" O   PRO R 292 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   ASN R 301 " --> pdb=" O   ILE R 297 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER R 302 " --> pdb=" O   SER R 298 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 317
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 74 through 76
      No H-bonds generated for 'chain 'S' and resid 74 through 76'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.557A  pdb=" N   ASP S  90 " --> pdb=" O   ARG S  87 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 87 through 91'
    Processing helix  chain 'D' and resid 21 through 27
      removed outlier: 4.368A  pdb=" N   HIS D  26 " --> pdb=" O   CYS D  21 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.148A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.535A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.773A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.919A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.866A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.620A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.610A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.843A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 5 through 7
      removed outlier: 3.536A  pdb=" N   SER S  23 " --> pdb=" O   VAL S   5 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR S  78 " --> pdb=" O   ASP S  73 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASP S  73 " --> pdb=" O   THR S  78 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.703A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 49 through 51
      removed outlier: 3.703A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.852A  pdb=" N   ASN S 194 " --> pdb=" O   ARG S 191 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU S 178 " --> pdb=" O   GLN S 186 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)

    409 hydrogen bonds defined for protein.
    1161 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: 2.68

  Time building geometry restraints manager: 3.06 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2910
        1.34 -     1.46: 1722
        1.46 -     1.58: 4556
        1.58 -     1.69: 0
        1.69 -     1.81: 100
  Bond restraints: 9288
  Sorted by residual:
  bond pdb=" C   ILE R  31 "
       pdb=" N   PRO R  32 "
    ideal  model  delta    sigma   weight residual
    1.335  1.369 -0.034 1.30e-02 5.92e+03 6.91e+00
  bond pdb=" N   VAL S   2 "
       pdb=" CA  VAL S   2 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.29e-02 6.01e+03 6.84e+00
  bond pdb=" N   ASP S   1 "
       pdb=" CA  ASP S   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.56e+00
  bond pdb=" CG1 ILE R 250 "
       pdb=" CD1 ILE R 250 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.46e+00
  bond pdb=" CB  CYS C  72 "
       pdb=" SG  CYS C  72 "
    ideal  model  delta    sigma   weight residual
    1.808  1.758  0.050 3.30e-02 9.18e+02 2.28e+00
  ... (remaining 9283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 12307
        1.88 -     3.77: 221
        3.77 -     5.65: 42
        5.65 -     7.54: 10
        7.54 -     9.42: 4
  Bond angle restraints: 12584
  Sorted by residual:
  angle pdb=" C   ILE R  34 "
        pdb=" N   TYR R  35 "
        pdb=" CA  TYR R  35 "
      ideal   model   delta    sigma   weight residual
     121.14  113.90    7.24 1.75e+00 3.27e-01 1.71e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.44    3.76 9.60e-01 1.09e+00 1.53e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  128.43   -6.89 1.91e+00 2.74e-01 1.30e+01
  angle pdb=" C   MET R 113 "
        pdb=" N   TYR R 114 "
        pdb=" CA  TYR R 114 "
      ideal   model   delta    sigma   weight residual
     120.68  114.97    5.71 1.70e+00 3.46e-01 1.13e+01
  angle pdb=" CA  MET R 187 "
        pdb=" CB  MET R 187 "
        pdb=" CG  MET R 187 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  ... (remaining 12579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 4949
       15.46 -    30.92: 437
       30.92 -    46.38: 99
       46.38 -    61.84: 13
       61.84 -    77.30: 2
  Dihedral angle restraints: 5500
    sinusoidal: 2140
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  THR B 164 "
           pdb=" C   THR B 164 "
           pdb=" N   THR B 165 "
           pdb=" CA  THR B 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  VAL D  29 "
           pdb=" C   VAL D  29 "
           pdb=" N   PRO D  30 "
           pdb=" CA  PRO D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.08  -21.92     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1054
       0.044 -    0.088: 276
       0.088 -    0.132: 78
       0.132 -    0.176: 9
       0.176 -    0.220: 4
  Chirality restraints: 1421
  Sorted by residual:
  chirality pdb=" CA  ASN R 305 "
            pdb=" N   ASN R 305 "
            pdb=" C   ASN R 305 "
            pdb=" CB  ASN R 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  VAL S   2 "
            pdb=" N   VAL S   2 "
            pdb=" C   VAL S   2 "
            pdb=" CB  VAL S   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  ILE S  58 "
            pdb=" CA  ILE S  58 "
            pdb=" CG1 ILE S  58 "
            pdb=" CG2 ILE S  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1418 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 235 "   -0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO S 236 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO S 236 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO S 236 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 150 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO S 151 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO S 151 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S 151 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 236 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 757
        2.74 -     3.28: 9303
        3.28 -     3.82: 15004
        3.82 -     4.36: 17273
        4.36 -     4.90: 30123
  Nonbonded interactions: 72460
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 290 "
            pdb=" O   SER A 293 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OH  TYR R 114 "
            pdb=" O   ALA R 157 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER B 122 "
            pdb=" OE2 GLU B 138 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" ND2 ASN B 237 "
            pdb=" OD1 ASN B 239 "
     model   vdw
     2.280 3.120
  ... (remaining 72455 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.550
  Find NCS groups from input model:        0.120
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6446
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      :  0.003   0.061   9289  Z= 0.153
  Angle     :  0.652   9.424  12586  Z= 0.350
  Chirality :  0.044   0.220   1421
  Planarity :  0.004   0.063   1590
  Dihedral  : 12.424  77.301   3331
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.57 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.97 (0.24), residues: 1142
  helix:  0.85 (0.27), residues: 372
  sheet: -0.08 (0.31), residues: 275
  loop : -2.21 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 195 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.013   0.001   TYR R 107 
 ARG   0.013   0.001   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16578 (  406)
  hydrogen bonds       : angle       6.75799 ( 1161)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.26399 (    2)
  covalent geometry    : bond        0.00326 ( 9288)
  covalent geometry    : angle       0.65238 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7772 (mptt) cc_final: 0.7254 (mptt)
REVERT: A   36 LEU cc_start: 0.7700 (mt) cc_final: 0.7466 (mp)
REVERT: A  194 LEU cc_start: 0.7963 (tp) cc_final: 0.7681 (tp)
REVERT: A  262 THR cc_start: 0.8384 (m) cc_final: 0.7787 (m)
REVERT: A  270 LYS cc_start: 0.7983 (mppt) cc_final: 0.7519 (mppt)
REVERT: A  275 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7094 (mt-10)
REVERT: A  317 LYS cc_start: 0.7103 (ptmt) cc_final: 0.6852 (ptmt)
REVERT: A  321 THR cc_start: 0.8149 (t) cc_final: 0.7907 (t)
REVERT: A  333 GLN cc_start: 0.7648 (tp40) cc_final: 0.7073 (tp40)
REVERT: A  348 LEU cc_start: 0.8315 (mm) cc_final: 0.8095 (mm)
REVERT: A  349 LYS cc_start: 0.8057 (mttm) cc_final: 0.7715 (mttm)
REVERT: B   22 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6486 (ptp-110)
REVERT: B   61 MET cc_start: 0.7313 (ppp) cc_final: 0.6766 (ppp)
REVERT: B  120 ILE cc_start: 0.8236 (pt) cc_final: 0.8033 (pt)
REVERT: B  155 ASN cc_start: 0.7044 (t0) cc_final: 0.6668 (t0)
REVERT: B  197 ARG cc_start: 0.6587 (mpt180) cc_final: 0.6367 (mpt180)
REVERT: B  228 ASP cc_start: 0.6776 (m-30) cc_final: 0.6542 (m-30)
REVERT: B  246 ASP cc_start: 0.6667 (t70) cc_final: 0.6343 (t70)
REVERT: B  247 ASP cc_start: 0.6194 (t0) cc_final: 0.5826 (t0)
REVERT: B  314 ARG cc_start: 0.6975 (mtp85) cc_final: 0.6699 (mtp85)
REVERT: B  325 MET cc_start: 0.6220 (mpp) cc_final: 0.5658 (mpp)
REVERT: C   52 MET cc_start: 0.7227 (tpt) cc_final: 0.6803 (tpt)
REVERT: R  129 LEU cc_start: 0.7409 (tp) cc_final: 0.7165 (tp)
REVERT: R  131 ILE cc_start: 0.8303 (mp) cc_final: 0.8084 (mp)
REVERT: R  187 MET cc_start: 0.4502 (pmm) cc_final: 0.3565 (pmm)
REVERT: R  289 ASN cc_start: 0.5309 (t0) cc_final: 0.3915 (t0)
REVERT: S   57 THR cc_start: 0.7925 (p) cc_final: 0.7721 (p)
REVERT: S  118 THR cc_start: 0.7889 (p) cc_final: 0.7643 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.2307
  time to fit residues: 83.4624
Evaluate side-chains
  259 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 88 optimal weight:    0.1980
   chunk 34 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0020
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 304 GLN
B  88 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.189056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.162363 restraints weight = 13510.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.85
r_work: 0.3888 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6696
moved from start:          0.1024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9289  Z= 0.140
  Angle     :  0.630   7.434  12586  Z= 0.334
  Chirality :  0.044   0.210   1421
  Planarity :  0.005   0.066   1590
  Dihedral  :  4.808  25.550   1261
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  8.97 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.77 (0.24), residues: 1142
  helix:  1.11 (0.27), residues: 375
  sheet:  0.17 (0.32), residues: 257
  loop : -2.21 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 195 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.013   0.001   PHE B 278 
 TYR   0.046   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  406)
  hydrogen bonds       : angle       5.27310 ( 1161)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.44375 (    2)
  covalent geometry    : bond        0.00305 ( 9288)
  covalent geometry    : angle       0.63007 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 267
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8005 (mptt) cc_final: 0.7357 (mptt)
REVERT: A   53 MET cc_start: 0.5958 (mmm) cc_final: 0.5694 (mmm)
REVERT: A  194 LEU cc_start: 0.8046 (tp) cc_final: 0.7732 (tp)
REVERT: A  262 THR cc_start: 0.8523 (m) cc_final: 0.8112 (m)
REVERT: A  270 LYS cc_start: 0.7918 (mppt) cc_final: 0.7416 (mppt)
REVERT: A  333 GLN cc_start: 0.8153 (tp40) cc_final: 0.7479 (tp40)
REVERT: A  349 LYS cc_start: 0.8194 (mttm) cc_final: 0.7861 (mttm)
REVERT: B   22 ARG cc_start: 0.7087 (ptp-110) cc_final: 0.6643 (ptp-110)
REVERT: B   46 ARG cc_start: 0.7096 (ptt-90) cc_final: 0.6643 (ptt-90)
REVERT: B   48 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6469 (mmm160)
REVERT: B   61 MET cc_start: 0.7590 (ppp) cc_final: 0.7360 (ppp)
REVERT: B  120 ILE cc_start: 0.8125 (pt) cc_final: 0.7766 (mt)
REVERT: B  155 ASN cc_start: 0.7703 (t0) cc_final: 0.7361 (t0)
REVERT: B  175 GLN cc_start: 0.7241 (mp10) cc_final: 0.6885 (mp10)
REVERT: B  228 ASP cc_start: 0.7182 (m-30) cc_final: 0.6949 (m-30)
REVERT: B  232 ILE cc_start: 0.8402 (mt) cc_final: 0.8064 (tp)
REVERT: B  246 ASP cc_start: 0.7330 (t70) cc_final: 0.6993 (t70)
REVERT: B  247 ASP cc_start: 0.7005 (t0) cc_final: 0.6504 (t0)
REVERT: B  314 ARG cc_start: 0.7263 (mtp85) cc_final: 0.7058 (mtp85)
REVERT: B  325 MET cc_start: 0.6935 (mpp) cc_final: 0.6206 (mpp)
REVERT: C   52 MET cc_start: 0.7969 (tpt) cc_final: 0.7365 (tpt)
REVERT: C   61 VAL cc_start: 0.7818 (t) cc_final: 0.7524 (p)
REVERT: C   69 MET cc_start: 0.6589 (mpp) cc_final: 0.6347 (mpp)
REVERT: R  131 ILE cc_start: 0.8357 (mp) cc_final: 0.8053 (mp)
REVERT: R  165 MET cc_start: 0.2528 (mmm) cc_final: 0.2240 (mmm)
REVERT: R  187 MET cc_start: 0.4614 (pmm) cc_final: 0.3841 (pmm)
REVERT: R  250 ILE cc_start: 0.7934 (mp) cc_final: 0.7607 (mp)
REVERT: R  289 ASN cc_start: 0.5515 (t0) cc_final: 0.4963 (t0)
REVERT: R  293 TYR cc_start: 0.6986 (m-80) cc_final: 0.6692 (m-80)
REVERT: S   52 SER cc_start: 0.8295 (t) cc_final: 0.8034 (p)
REVERT: S   57 THR cc_start: 0.8110 (p) cc_final: 0.7860 (p)
REVERT: S   80 PHE cc_start: 0.7944 (m-80) cc_final: 0.7503 (m-80)
REVERT: S   95 TYR cc_start: 0.8325 (m-80) cc_final: 0.7991 (m-80)
REVERT: S  118 THR cc_start: 0.7872 (p) cc_final: 0.7662 (p)
  outliers start: 9
  outliers final: 6
  residues processed: 270
  average time/residue: 0.2370
  time to fit residues: 86.9546
Evaluate side-chains
  266 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 260
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 60 optimal weight:    0.0040
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0970
   chunk 61 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 132 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.189379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.162152 restraints weight = 13639.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 2.88
r_work: 0.3880 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9289  Z= 0.134
  Angle     :  0.598   7.820  12586  Z= 0.317
  Chirality :  0.043   0.197   1421
  Planarity :  0.004   0.062   1590
  Dihedral  :  4.765  25.355   1261
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.60 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.73 (0.24), residues: 1142
  helix:  1.25 (0.27), residues: 375
  sheet: -0.00 (0.32), residues: 249
  loop : -2.12 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.020   0.001   PHE S  68 
 TYR   0.046   0.002   TYR R 114 
 ARG   0.007   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  406)
  hydrogen bonds       : angle       4.94013 ( 1161)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.34475 (    2)
  covalent geometry    : bond        0.00295 ( 9288)
  covalent geometry    : angle       0.59832 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 266
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7985 (mptt) cc_final: 0.7314 (mptt)
REVERT: A   53 MET cc_start: 0.5808 (mmm) cc_final: 0.5554 (mmm)
REVERT: A  194 LEU cc_start: 0.8022 (tp) cc_final: 0.7710 (tp)
REVERT: A  240 MET cc_start: 0.6846 (mtm) cc_final: 0.6585 (mtp)
REVERT: A  270 LYS cc_start: 0.7910 (mppt) cc_final: 0.7442 (mppt)
REVERT: A  271 LYS cc_start: 0.7516 (tttt) cc_final: 0.7129 (mttt)
REVERT: A  333 GLN cc_start: 0.8155 (tp40) cc_final: 0.7481 (tp40)
REVERT: A  348 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8265 (mm)
REVERT: A  349 LYS cc_start: 0.8207 (mttm) cc_final: 0.7880 (mttm)
REVERT: B   46 ARG cc_start: 0.7144 (ptt-90) cc_final: 0.6657 (ptt-90)
REVERT: B   47 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8077 (m)
REVERT: B   48 ARG cc_start: 0.7672 (mmm160) cc_final: 0.6582 (mmm160)
REVERT: B   68 ARG cc_start: 0.8146 (ttt-90) cc_final: 0.7515 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7937 (t0) cc_final: 0.7331 (t0)
REVERT: B  120 ILE cc_start: 0.8136 (pt) cc_final: 0.7841 (mt)
REVERT: B  155 ASN cc_start: 0.7758 (t0) cc_final: 0.7468 (t0)
REVERT: B  175 GLN cc_start: 0.7190 (mp10) cc_final: 0.6814 (mp10)
REVERT: B  204 CYS cc_start: 0.8026 (p) cc_final: 0.7094 (p)
REVERT: B  228 ASP cc_start: 0.7250 (m-30) cc_final: 0.6961 (m-30)
REVERT: B  232 ILE cc_start: 0.8388 (mt) cc_final: 0.8091 (tp)
REVERT: B  246 ASP cc_start: 0.7353 (t70) cc_final: 0.6999 (t70)
REVERT: B  293 ASN cc_start: 0.8398 (p0) cc_final: 0.8135 (p0)
REVERT: B  325 MET cc_start: 0.7020 (mpp) cc_final: 0.6225 (mpp)
REVERT: C   52 MET cc_start: 0.7973 (tpt) cc_final: 0.7401 (tpt)
REVERT: C   69 MET cc_start: 0.6565 (mpp) cc_final: 0.6316 (mpp)
REVERT: R  131 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7995 (mp)
REVERT: R  165 MET cc_start: 0.2597 (mmm) cc_final: 0.2314 (mmm)
REVERT: R  187 MET cc_start: 0.4551 (pmm) cc_final: 0.4142 (pmm)
REVERT: R  245 ARG cc_start: 0.6248 (ptt180) cc_final: 0.5998 (ptt180)
REVERT: R  246 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6433 (tp)
REVERT: R  250 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7642 (mp)
REVERT: R  289 ASN cc_start: 0.5567 (t0) cc_final: 0.4734 (t0)
REVERT: R  293 TYR cc_start: 0.7019 (m-80) cc_final: 0.6722 (m-80)
REVERT: S   52 SER cc_start: 0.8273 (t) cc_final: 0.7769 (p)
REVERT: S   80 PHE cc_start: 0.7886 (m-80) cc_final: 0.7538 (m-80)
REVERT: S  116 THR cc_start: 0.8124 (p) cc_final: 0.7921 (t)
  outliers start: 19
  outliers final: 9
  residues processed: 274
  average time/residue: 0.2312
  time to fit residues: 85.5224
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 265
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  199 VAL
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 107 optimal weight:    0.2980
   chunk 44 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 85 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.188701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.161472 restraints weight = 13576.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 2.89
r_work: 0.3869 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9289  Z= 0.158
  Angle     :  0.606   9.799  12586  Z= 0.318
  Chirality :  0.043   0.198   1421
  Planarity :  0.004   0.061   1590
  Dihedral  :  4.777  26.054   1261
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.22 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.02 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.71 (0.24), residues: 1142
  helix:  1.29 (0.27), residues: 375
  sheet: -0.12 (0.32), residues: 251
  loop : -2.07 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.016   0.001   PHE B 278 
 TYR   0.047   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  406)
  hydrogen bonds       : angle       4.87870 ( 1161)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.36018 (    2)
  covalent geometry    : bond        0.00354 ( 9288)
  covalent geometry    : angle       0.60618 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 273
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.8015 (mptt) cc_final: 0.7319 (mptt)
REVERT: A   53 MET cc_start: 0.5811 (mmm) cc_final: 0.5600 (mmm)
REVERT: A  194 LEU cc_start: 0.8027 (tp) cc_final: 0.7692 (tp)
REVERT: A  240 MET cc_start: 0.6833 (mtm) cc_final: 0.6541 (mtp)
REVERT: A  270 LYS cc_start: 0.7879 (mppt) cc_final: 0.7383 (mppt)
REVERT: A  271 LYS cc_start: 0.7502 (tttt) cc_final: 0.7122 (mttt)
REVERT: A  333 GLN cc_start: 0.8151 (tp40) cc_final: 0.7481 (tp40)
REVERT: A  336 PHE cc_start: 0.8045 (t80) cc_final: 0.7713 (t80)
REVERT: A  348 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (mm)
REVERT: A  349 LYS cc_start: 0.8221 (mttm) cc_final: 0.7879 (mttm)
REVERT: B   22 ARG cc_start: 0.7102 (ptp-110) cc_final: 0.6806 (ptp-170)
REVERT: B   46 ARG cc_start: 0.7256 (ptt-90) cc_final: 0.6750 (ptt-90)
REVERT: B   47 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8129 (m)
REVERT: B   48 ARG cc_start: 0.7741 (mmm160) cc_final: 0.6665 (mmm160)
REVERT: B   86 THR cc_start: 0.8183 (p) cc_final: 0.7915 (p)
REVERT: B   88 ASN cc_start: 0.7972 (m110) cc_final: 0.7650 (m-40)
REVERT: B   97 SER cc_start: 0.8253 (t) cc_final: 0.7963 (p)
REVERT: B  120 ILE cc_start: 0.8101 (pt) cc_final: 0.7886 (mt)
REVERT: B  132 ASN cc_start: 0.7219 (p0) cc_final: 0.6988 (p0)
REVERT: B  155 ASN cc_start: 0.7735 (t0) cc_final: 0.7422 (t0)
REVERT: B  175 GLN cc_start: 0.7227 (mp10) cc_final: 0.6859 (mp10)
REVERT: B  204 CYS cc_start: 0.8046 (p) cc_final: 0.7084 (p)
REVERT: B  228 ASP cc_start: 0.7264 (m-30) cc_final: 0.6912 (m-30)
REVERT: B  230 ASN cc_start: 0.7878 (m-40) cc_final: 0.7619 (m110)
REVERT: B  232 ILE cc_start: 0.8389 (mt) cc_final: 0.8142 (tp)
REVERT: B  246 ASP cc_start: 0.7419 (t70) cc_final: 0.7048 (t70)
REVERT: B  293 ASN cc_start: 0.8453 (p0) cc_final: 0.8099 (p0)
REVERT: B  323 ASP cc_start: 0.7347 (t0) cc_final: 0.7018 (t0)
REVERT: B  325 MET cc_start: 0.7211 (mpp) cc_final: 0.6303 (mpp)
REVERT: C   52 MET cc_start: 0.7948 (tpt) cc_final: 0.7393 (tpt)
REVERT: C   69 MET cc_start: 0.6612 (mpp) cc_final: 0.6242 (mpp)
REVERT: R  131 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7985 (mp)
REVERT: R  183 MET cc_start: 0.5145 (mtt) cc_final: 0.4807 (mtt)
REVERT: R  187 MET cc_start: 0.5858 (pmm) cc_final: 0.5172 (pmm)
REVERT: R  245 ARG cc_start: 0.6308 (ptt180) cc_final: 0.6053 (ptt180)
REVERT: R  246 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6471 (tp)
REVERT: R  250 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7758 (mp)
REVERT: R  289 ASN cc_start: 0.5679 (t0) cc_final: 0.4665 (t0)
REVERT: R  293 TYR cc_start: 0.7044 (m-80) cc_final: 0.6733 (m-80)
REVERT: S   52 SER cc_start: 0.8326 (t) cc_final: 0.7944 (p)
REVERT: S   80 PHE cc_start: 0.7821 (m-80) cc_final: 0.7521 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 282
  average time/residue: 0.2265
  time to fit residues: 86.0737
Evaluate side-chains
  277 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 263
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 107 optimal weight:    0.1980
   chunk 34 optimal weight:    0.4980
   chunk 87 optimal weight:    0.9990
   chunk 50 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.189213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.162004 restraints weight = 13580.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.87
r_work: 0.3873 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9289  Z= 0.144
  Angle     :  0.598   8.115  12586  Z= 0.316
  Chirality :  0.043   0.185   1421
  Planarity :  0.004   0.060   1590
  Dihedral  :  4.746  27.932   1261
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.48 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.13 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.25), residues: 1142
  helix:  1.35 (0.27), residues: 375
  sheet: -0.11 (0.32), residues: 253
  loop : -2.05 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.017   0.001   PHE A 274 
 TYR   0.050   0.002   TYR R 114 
 ARG   0.005   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  406)
  hydrogen bonds       : angle       4.76219 ( 1161)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       1.72167 (    2)
  covalent geometry    : bond        0.00321 ( 9288)
  covalent geometry    : angle       0.59760 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 261
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7996 (mptt) cc_final: 0.7269 (mptt)
REVERT: A  194 LEU cc_start: 0.8037 (tp) cc_final: 0.7691 (tp)
REVERT: A  240 MET cc_start: 0.6789 (mtm) cc_final: 0.6505 (mtp)
REVERT: A  243 MET cc_start: 0.7526 (tpp) cc_final: 0.6680 (tpp)
REVERT: A  270 LYS cc_start: 0.7847 (mppt) cc_final: 0.7375 (mppt)
REVERT: A  271 LYS cc_start: 0.7463 (tttt) cc_final: 0.7097 (mttt)
REVERT: A  333 GLN cc_start: 0.8173 (tp40) cc_final: 0.7506 (tp40)
REVERT: A  336 PHE cc_start: 0.8051 (t80) cc_final: 0.7715 (t80)
REVERT: A  348 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8237 (mm)
REVERT: A  349 LYS cc_start: 0.8187 (mttm) cc_final: 0.7861 (mttm)
REVERT: B   22 ARG cc_start: 0.7058 (ptp-110) cc_final: 0.6776 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7536 (tp40) cc_final: 0.7268 (tp40)
REVERT: B   46 ARG cc_start: 0.7254 (ptt-90) cc_final: 0.6779 (ptt-90)
REVERT: B   47 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8155 (m)
REVERT: B   48 ARG cc_start: 0.7664 (mmm160) cc_final: 0.6557 (mmm160)
REVERT: B   86 THR cc_start: 0.8179 (p) cc_final: 0.7905 (p)
REVERT: B   88 ASN cc_start: 0.7935 (m110) cc_final: 0.7621 (m-40)
REVERT: B  120 ILE cc_start: 0.8118 (pt) cc_final: 0.7914 (mt)
REVERT: B  132 ASN cc_start: 0.7166 (p0) cc_final: 0.6943 (p0)
REVERT: B  155 ASN cc_start: 0.7753 (t0) cc_final: 0.7423 (t0)
REVERT: B  175 GLN cc_start: 0.7163 (mp10) cc_final: 0.6785 (mp10)
REVERT: B  204 CYS cc_start: 0.8021 (p) cc_final: 0.7027 (p)
REVERT: B  228 ASP cc_start: 0.7282 (m-30) cc_final: 0.6907 (m-30)
REVERT: B  230 ASN cc_start: 0.7893 (m-40) cc_final: 0.7627 (m110)
REVERT: B  232 ILE cc_start: 0.8398 (mt) cc_final: 0.8128 (tp)
REVERT: B  246 ASP cc_start: 0.7400 (t70) cc_final: 0.7051 (t70)
REVERT: B  293 ASN cc_start: 0.8461 (p0) cc_final: 0.8118 (p0)
REVERT: B  323 ASP cc_start: 0.7366 (t0) cc_final: 0.6945 (t0)
REVERT: B  325 MET cc_start: 0.7218 (mpp) cc_final: 0.6348 (mpp)
REVERT: C   52 MET cc_start: 0.7979 (tpt) cc_final: 0.7411 (tpt)
REVERT: C   69 MET cc_start: 0.6645 (mpp) cc_final: 0.6271 (mpp)
REVERT: R  131 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7991 (mp)
REVERT: R  183 MET cc_start: 0.5103 (mtt) cc_final: 0.4746 (mtt)
REVERT: R  187 MET cc_start: 0.5455 (pmm) cc_final: 0.4745 (pmm)
REVERT: R  245 ARG cc_start: 0.6291 (ptt180) cc_final: 0.6036 (ptt180)
REVERT: R  246 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6453 (tp)
REVERT: R  250 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7752 (mp)
REVERT: R  289 ASN cc_start: 0.5542 (t0) cc_final: 0.4502 (t0)
REVERT: R  293 TYR cc_start: 0.6997 (m-80) cc_final: 0.6691 (m-80)
REVERT: S   52 SER cc_start: 0.8262 (t) cc_final: 0.7998 (p)
REVERT: S   78 THR cc_start: 0.8437 (m) cc_final: 0.7999 (t)
REVERT: S   80 PHE cc_start: 0.7801 (m-80) cc_final: 0.7429 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 272
  average time/residue: 0.2307
  time to fit residues: 84.9448
Evaluate side-chains
  273 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 259
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.189038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.161878 restraints weight = 13521.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 2.87
r_work: 0.3872 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9289  Z= 0.156
  Angle     :  0.605   8.293  12586  Z= 0.320
  Chirality :  0.043   0.186   1421
  Planarity :  0.004   0.060   1590
  Dihedral  :  4.770  29.120   1261
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.13 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.74 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.69 (0.25), residues: 1142
  helix:  1.34 (0.27), residues: 375
  sheet: -0.15 (0.33), residues: 253
  loop : -2.06 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 258 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.016   0.001   PHE B 278 
 TYR   0.052   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  406)
  hydrogen bonds       : angle       4.78132 ( 1161)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       0.98212 (    2)
  covalent geometry    : bond        0.00349 ( 9288)
  covalent geometry    : angle       0.60532 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 257
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7988 (mptt) cc_final: 0.7254 (mptt)
REVERT: A  194 LEU cc_start: 0.8031 (tp) cc_final: 0.7712 (tp)
REVERT: A  240 MET cc_start: 0.6779 (mtm) cc_final: 0.6487 (mtp)
REVERT: A  243 MET cc_start: 0.7540 (tpp) cc_final: 0.6680 (tpp)
REVERT: A  270 LYS cc_start: 0.7838 (mppt) cc_final: 0.7370 (mppt)
REVERT: A  271 LYS cc_start: 0.7456 (tttt) cc_final: 0.7110 (mttt)
REVERT: A  333 GLN cc_start: 0.8172 (tp40) cc_final: 0.7523 (tp40)
REVERT: A  348 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8293 (mm)
REVERT: A  349 LYS cc_start: 0.8196 (mttm) cc_final: 0.7875 (mttm)
REVERT: B   22 ARG cc_start: 0.7076 (ptp-110) cc_final: 0.6831 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7543 (tp40) cc_final: 0.7259 (tp40)
REVERT: B   46 ARG cc_start: 0.7276 (ptt-90) cc_final: 0.6865 (ptt-90)
REVERT: B   47 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8165 (m)
REVERT: B   48 ARG cc_start: 0.7741 (mmm160) cc_final: 0.6861 (mmm160)
REVERT: B   68 ARG cc_start: 0.8154 (ttt-90) cc_final: 0.7781 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7882 (t0) cc_final: 0.7458 (t0)
REVERT: B   86 THR cc_start: 0.8195 (p) cc_final: 0.7890 (p)
REVERT: B   88 ASN cc_start: 0.7969 (m110) cc_final: 0.7631 (m-40)
REVERT: B  132 ASN cc_start: 0.7104 (p0) cc_final: 0.6886 (p0)
REVERT: B  155 ASN cc_start: 0.7806 (t0) cc_final: 0.7407 (t0)
REVERT: B  175 GLN cc_start: 0.7164 (mp10) cc_final: 0.6767 (mp10)
REVERT: B  204 CYS cc_start: 0.8031 (p) cc_final: 0.7062 (p)
REVERT: B  228 ASP cc_start: 0.7292 (m-30) cc_final: 0.6911 (m-30)
REVERT: B  230 ASN cc_start: 0.7896 (m-40) cc_final: 0.7619 (m110)
REVERT: B  232 ILE cc_start: 0.8392 (mt) cc_final: 0.8119 (tp)
REVERT: B  246 ASP cc_start: 0.7443 (t70) cc_final: 0.7071 (t70)
REVERT: B  293 ASN cc_start: 0.8497 (p0) cc_final: 0.8153 (p0)
REVERT: C   52 MET cc_start: 0.8017 (tpt) cc_final: 0.7443 (tpt)
REVERT: C   69 MET cc_start: 0.6591 (mpp) cc_final: 0.6203 (mpp)
REVERT: R  131 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7979 (mp)
REVERT: R  183 MET cc_start: 0.5138 (mtt) cc_final: 0.4770 (mtt)
REVERT: R  187 MET cc_start: 0.5708 (pmm) cc_final: 0.4909 (pmm)
REVERT: R  245 ARG cc_start: 0.6239 (ptt180) cc_final: 0.5979 (ptt180)
REVERT: R  246 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6459 (tp)
REVERT: R  250 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (mp)
REVERT: R  289 ASN cc_start: 0.5626 (t0) cc_final: 0.4556 (t0)
REVERT: R  293 TYR cc_start: 0.6971 (m-80) cc_final: 0.6691 (m-80)
REVERT: S   52 SER cc_start: 0.8245 (t) cc_final: 0.7965 (p)
REVERT: S   78 THR cc_start: 0.8414 (m) cc_final: 0.7964 (t)
REVERT: S   80 PHE cc_start: 0.7816 (m-80) cc_final: 0.7420 (m-80)
REVERT: S  234 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5773 (pp20)
  outliers start: 18
  outliers final: 10
  residues processed: 268
  average time/residue: 0.2287
  time to fit residues: 82.0370
Evaluate side-chains
  272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 256
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 106 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 80 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9990
   chunk 66 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.189032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.161925 restraints weight = 13726.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 2.92
r_work: 0.3872 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9289  Z= 0.145
  Angle     :  0.614   8.630  12586  Z= 0.323
  Chirality :  0.043   0.201   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.794  34.091   1261
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.04 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.15 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1142
  helix:  1.40 (0.27), residues: 375
  sheet: -0.19 (0.33), residues: 253
  loop : -2.07 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 211 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 234 
 TYR   0.049   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  406)
  hydrogen bonds       : angle       4.74176 ( 1161)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       1.08585 (    2)
  covalent geometry    : bond        0.00324 ( 9288)
  covalent geometry    : angle       0.61391 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 258
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7988 (mptt) cc_final: 0.7245 (mptt)
REVERT: A  194 LEU cc_start: 0.8010 (tp) cc_final: 0.7685 (tp)
REVERT: A  197 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7633 (mmmm)
REVERT: A  240 MET cc_start: 0.6824 (mtm) cc_final: 0.6508 (mtp)
REVERT: A  243 MET cc_start: 0.7536 (tpp) cc_final: 0.6694 (tpp)
REVERT: A  270 LYS cc_start: 0.7819 (mppt) cc_final: 0.7352 (mppt)
REVERT: A  271 LYS cc_start: 0.7450 (tttt) cc_final: 0.7110 (mttt)
REVERT: A  333 GLN cc_start: 0.8167 (tp40) cc_final: 0.7501 (tp40)
REVERT: A  348 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8272 (mm)
REVERT: A  349 LYS cc_start: 0.8189 (mttm) cc_final: 0.7853 (mttm)
REVERT: B   22 ARG cc_start: 0.7074 (ptp-110) cc_final: 0.6829 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7535 (tp40) cc_final: 0.7244 (tp40)
REVERT: B   46 ARG cc_start: 0.7271 (ptt-90) cc_final: 0.6943 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7744 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7927 (t0) cc_final: 0.7485 (t0)
REVERT: B   86 THR cc_start: 0.8169 (p) cc_final: 0.7876 (p)
REVERT: B   88 ASN cc_start: 0.7985 (m110) cc_final: 0.7646 (m-40)
REVERT: B   97 SER cc_start: 0.8266 (t) cc_final: 0.7978 (p)
REVERT: B  132 ASN cc_start: 0.7119 (p0) cc_final: 0.6889 (p0)
REVERT: B  155 ASN cc_start: 0.7802 (t0) cc_final: 0.7397 (t0)
REVERT: B  175 GLN cc_start: 0.7152 (mp10) cc_final: 0.6729 (mp10)
REVERT: B  204 CYS cc_start: 0.8002 (p) cc_final: 0.7018 (p)
REVERT: B  228 ASP cc_start: 0.7299 (m-30) cc_final: 0.6911 (m-30)
REVERT: B  230 ASN cc_start: 0.7912 (m-40) cc_final: 0.7626 (m110)
REVERT: B  232 ILE cc_start: 0.8408 (mt) cc_final: 0.8136 (tp)
REVERT: B  246 ASP cc_start: 0.7477 (t70) cc_final: 0.7116 (t70)
REVERT: B  293 ASN cc_start: 0.8507 (p0) cc_final: 0.8177 (p0)
REVERT: C   52 MET cc_start: 0.8004 (tpt) cc_final: 0.7436 (tpt)
REVERT: C   69 MET cc_start: 0.6574 (mpp) cc_final: 0.6099 (mpp)
REVERT: R  131 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7979 (mp)
REVERT: R  183 MET cc_start: 0.5173 (mtt) cc_final: 0.4753 (mtt)
REVERT: R  187 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.4945 (pmm)
REVERT: R  245 ARG cc_start: 0.6253 (ptt180) cc_final: 0.5984 (ptt180)
REVERT: R  246 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6450 (tp)
REVERT: R  250 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7754 (mp)
REVERT: R  289 ASN cc_start: 0.5699 (t0) cc_final: 0.4640 (t0)
REVERT: R  293 TYR cc_start: 0.6963 (m-80) cc_final: 0.6702 (m-80)
REVERT: R  299 TYR cc_start: 0.6597 (m-10) cc_final: 0.6171 (m-80)
REVERT: S   52 SER cc_start: 0.8227 (t) cc_final: 0.7950 (p)
REVERT: S   78 THR cc_start: 0.8413 (m) cc_final: 0.7960 (t)
REVERT: S   80 PHE cc_start: 0.7786 (m-80) cc_final: 0.7345 (m-80)
REVERT: S  234 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5924 (pp20)
  outliers start: 21
  outliers final: 12
  residues processed: 269
  average time/residue: 0.2534
  time to fit residues: 91.2926
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 257
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.189019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.162006 restraints weight = 13880.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 2.96
r_work: 0.3864 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9289  Z= 0.154
  Angle     :  0.622   8.596  12586  Z= 0.328
  Chirality :  0.043   0.191   1421
  Planarity :  0.005   0.059   1590
  Dihedral  :  4.834  34.103   1261
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.30 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.95 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.76 (0.24), residues: 1142
  helix:  1.35 (0.27), residues: 376
  sheet: -0.20 (0.32), residues: 248
  loop : -2.14 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A 213 
 PHE   0.015   0.001   PHE R  39 
 TYR   0.050   0.002   TYR R 114 
 ARG   0.007   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03953 (  406)
  hydrogen bonds       : angle       4.74097 ( 1161)
  SS BOND              : bond        0.00181 (    1)
  SS BOND              : angle       0.99535 (    2)
  covalent geometry    : bond        0.00345 ( 9288)
  covalent geometry    : angle       0.62170 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 256
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 LYS cc_start: 0.7934 (mptt) cc_final: 0.7158 (mptt)
REVERT: A  194 LEU cc_start: 0.8020 (tp) cc_final: 0.7694 (tp)
REVERT: A  240 MET cc_start: 0.6799 (mtm) cc_final: 0.6546 (mtp)
REVERT: A  243 MET cc_start: 0.7575 (tpp) cc_final: 0.6714 (tpp)
REVERT: A  270 LYS cc_start: 0.7848 (mppt) cc_final: 0.7377 (mppt)
REVERT: A  271 LYS cc_start: 0.7448 (tttt) cc_final: 0.7098 (mttt)
REVERT: A  312 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7905 (mmtt)
REVERT: A  333 GLN cc_start: 0.8188 (tp40) cc_final: 0.7518 (tp40)
REVERT: A  348 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8230 (mm)
REVERT: A  349 LYS cc_start: 0.8201 (mttm) cc_final: 0.7864 (mttm)
REVERT: B   22 ARG cc_start: 0.7102 (ptp-110) cc_final: 0.6850 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7521 (tp40) cc_final: 0.7223 (tp40)
REVERT: B   46 ARG cc_start: 0.7231 (ptt-90) cc_final: 0.6960 (ptt-90)
REVERT: B   48 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7288 (mmm160)
REVERT: B   68 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7706 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7952 (t0) cc_final: 0.7498 (t0)
REVERT: B   86 THR cc_start: 0.8210 (p) cc_final: 0.7947 (p)
REVERT: B   88 ASN cc_start: 0.8004 (m110) cc_final: 0.7707 (m-40)
REVERT: B   97 SER cc_start: 0.8276 (t) cc_final: 0.7982 (p)
REVERT: B  132 ASN cc_start: 0.7152 (p0) cc_final: 0.6927 (p0)
REVERT: B  155 ASN cc_start: 0.7795 (t0) cc_final: 0.7375 (t0)
REVERT: B  175 GLN cc_start: 0.7171 (mp10) cc_final: 0.6758 (mp10)
REVERT: B  204 CYS cc_start: 0.8076 (p) cc_final: 0.7069 (p)
REVERT: B  228 ASP cc_start: 0.7320 (m-30) cc_final: 0.6926 (m-30)
REVERT: B  230 ASN cc_start: 0.7934 (m-40) cc_final: 0.7634 (m110)
REVERT: B  232 ILE cc_start: 0.8366 (mt) cc_final: 0.8109 (tp)
REVERT: B  246 ASP cc_start: 0.7517 (t70) cc_final: 0.7151 (t70)
REVERT: B  293 ASN cc_start: 0.8500 (p0) cc_final: 0.8170 (p0)
REVERT: B  325 MET cc_start: 0.7314 (mpp) cc_final: 0.6584 (mpp)
REVERT: C   52 MET cc_start: 0.8029 (tpt) cc_final: 0.7462 (tpt)
REVERT: C   69 MET cc_start: 0.6552 (mpp) cc_final: 0.6083 (mpp)
REVERT: R  131 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: R  187 MET cc_start: 0.5795 (OUTLIER) cc_final: 0.4997 (pmm)
REVERT: R  245 ARG cc_start: 0.6252 (ptt180) cc_final: 0.5902 (ppt170)
REVERT: R  246 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6464 (tp)
REVERT: R  250 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: R  289 ASN cc_start: 0.5746 (t0) cc_final: 0.4945 (t0)
REVERT: R  293 TYR cc_start: 0.7066 (m-80) cc_final: 0.6786 (m-80)
REVERT: R  299 TYR cc_start: 0.6631 (m-10) cc_final: 0.6170 (m-80)
REVERT: S   39 GLN cc_start: 0.8143 (tp40) cc_final: 0.7889 (tp40)
REVERT: S   52 SER cc_start: 0.8207 (t) cc_final: 0.7943 (p)
REVERT: S   78 THR cc_start: 0.8406 (m) cc_final: 0.7838 (t)
REVERT: S   80 PHE cc_start: 0.7702 (m-80) cc_final: 0.7274 (m-80)
REVERT: S  234 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5923 (pp20)
  outliers start: 20
  outliers final: 12
  residues processed: 267
  average time/residue: 0.2272
  time to fit residues: 81.3656
Evaluate side-chains
  274 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 256
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 105 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.188535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.161293 restraints weight = 13589.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 2.91
r_work: 0.3857 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9289  Z= 0.175
  Angle     :  0.651   8.788  12586  Z= 0.342
  Chirality :  0.044   0.199   1421
  Planarity :  0.005   0.059   1590
  Dihedral  :  4.909  34.993   1261
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.48 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.35 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.78 (0.25), residues: 1142
  helix:  1.32 (0.27), residues: 376
  sheet: -0.23 (0.33), residues: 250
  loop : -2.14 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.016   0.001   PHE B 278 
 TYR   0.057   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  406)
  hydrogen bonds       : angle       4.72393 ( 1161)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       4.04263 (    2)
  covalent geometry    : bond        0.00395 ( 9288)
  covalent geometry    : angle       0.64865 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 255
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LEU cc_start: 0.8020 (tp) cc_final: 0.7695 (tp)
REVERT: A  243 MET cc_start: 0.7565 (tpp) cc_final: 0.6788 (tpp)
REVERT: A  270 LYS cc_start: 0.7873 (mppt) cc_final: 0.7346 (mppt)
REVERT: A  271 LYS cc_start: 0.7454 (tttt) cc_final: 0.7070 (mttt)
REVERT: A  312 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7940 (mmtt)
REVERT: A  333 GLN cc_start: 0.8179 (tp40) cc_final: 0.7539 (tp40)
REVERT: A  348 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8246 (mm)
REVERT: A  349 LYS cc_start: 0.8204 (mttm) cc_final: 0.7866 (mttm)
REVERT: B   22 ARG cc_start: 0.7075 (ptp-110) cc_final: 0.6843 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7530 (tp40) cc_final: 0.7232 (tp40)
REVERT: B   46 ARG cc_start: 0.7236 (ptt-90) cc_final: 0.6944 (ptt-90)
REVERT: B   48 ARG cc_start: 0.7815 (mmm160) cc_final: 0.7300 (mmm160)
REVERT: B   68 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7744 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7940 (t0) cc_final: 0.7492 (t0)
REVERT: B   86 THR cc_start: 0.8333 (p) cc_final: 0.7976 (p)
REVERT: B   88 ASN cc_start: 0.8027 (m110) cc_final: 0.7646 (m-40)
REVERT: B  132 ASN cc_start: 0.7164 (p0) cc_final: 0.6958 (p0)
REVERT: B  155 ASN cc_start: 0.7783 (t0) cc_final: 0.7360 (t0)
REVERT: B  204 CYS cc_start: 0.8051 (p) cc_final: 0.7129 (p)
REVERT: B  228 ASP cc_start: 0.7314 (m-30) cc_final: 0.6943 (m-30)
REVERT: B  230 ASN cc_start: 0.7907 (m-40) cc_final: 0.7601 (m110)
REVERT: B  232 ILE cc_start: 0.8411 (mt) cc_final: 0.8128 (tp)
REVERT: B  246 ASP cc_start: 0.7452 (t70) cc_final: 0.7102 (t70)
REVERT: B  293 ASN cc_start: 0.8529 (p0) cc_final: 0.8212 (p0)
REVERT: B  325 MET cc_start: 0.7311 (mpp) cc_final: 0.6688 (mpp)
REVERT: C   52 MET cc_start: 0.7971 (tpt) cc_final: 0.7429 (tpt)
REVERT: C   69 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.6080 (mpp)
REVERT: R  131 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: R  183 MET cc_start: 0.5037 (mtt) cc_final: 0.4776 (mtt)
REVERT: R  187 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5002 (pmm)
REVERT: R  245 ARG cc_start: 0.6227 (ptt180) cc_final: 0.5871 (ppt170)
REVERT: R  246 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6491 (tp)
REVERT: R  250 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7785 (mp)
REVERT: R  289 ASN cc_start: 0.5833 (t0) cc_final: 0.4907 (t0)
REVERT: R  293 TYR cc_start: 0.7028 (m-80) cc_final: 0.6765 (m-80)
REVERT: S   39 GLN cc_start: 0.8145 (tp40) cc_final: 0.7870 (tp40)
REVERT: S   52 SER cc_start: 0.8225 (t) cc_final: 0.7945 (p)
REVERT: S   78 THR cc_start: 0.8411 (m) cc_final: 0.7847 (t)
REVERT: S   80 PHE cc_start: 0.7755 (m-80) cc_final: 0.7328 (m-80)
REVERT: S  234 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5855 (pp20)
  outliers start: 23
  outliers final: 12
  residues processed: 270
  average time/residue: 0.2977
  time to fit residues: 110.6709
Evaluate side-chains
  272 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 253
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 101 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 92 optimal weight:    0.5980
   chunk 99 optimal weight:    0.4980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.189024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.161498 restraints weight = 13606.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.4000 rms_B_bonded: 2.89
r_work: 0.3863 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9289  Z= 0.157
  Angle     :  0.654   8.901  12586  Z= 0.341
  Chirality :  0.044   0.195   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.879  34.985   1261
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.65 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.35 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.74 (0.25), residues: 1142
  helix:  1.31 (0.27), residues: 376
  sheet: -0.16 (0.33), residues: 248
  loop : -2.10 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S 176 
 HIS   0.003   0.001   HIS A 213 
 PHE   0.029   0.001   PHE A 274 
 TYR   0.060   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  406)
  hydrogen bonds       : angle       4.72913 ( 1161)
  SS BOND              : bond        0.00362 (    1)
  SS BOND              : angle       3.97475 (    2)
  covalent geometry    : bond        0.00357 ( 9288)
  covalent geometry    : angle       0.65175 (12584)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 LEU cc_start: 0.8075 (tp) cc_final: 0.7757 (tp)
REVERT: A  243 MET cc_start: 0.7589 (tpp) cc_final: 0.6746 (tpp)
REVERT: A  270 LYS cc_start: 0.7867 (mppt) cc_final: 0.7343 (mppt)
REVERT: A  271 LYS cc_start: 0.7441 (tttt) cc_final: 0.7144 (mttt)
REVERT: A  275 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: A  312 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7903 (mmtt)
REVERT: A  333 GLN cc_start: 0.8152 (tp40) cc_final: 0.7507 (tp40)
REVERT: A  348 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8259 (mm)
REVERT: A  349 LYS cc_start: 0.8223 (mttm) cc_final: 0.7889 (mttm)
REVERT: B   22 ARG cc_start: 0.7149 (ptp-110) cc_final: 0.6869 (ptp-170)
REVERT: B   32 GLN cc_start: 0.7444 (tp40) cc_final: 0.7175 (tp40)
REVERT: B   46 ARG cc_start: 0.7314 (ptt-90) cc_final: 0.6914 (ptt-90)
REVERT: B   68 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7765 (ttt-90)
REVERT: B   83 ASP cc_start: 0.7876 (t0) cc_final: 0.7414 (t0)
REVERT: B   86 THR cc_start: 0.8295 (p) cc_final: 0.7909 (p)
REVERT: B   88 ASN cc_start: 0.8013 (m110) cc_final: 0.7632 (m-40)
REVERT: B  132 ASN cc_start: 0.7165 (p0) cc_final: 0.6963 (p0)
REVERT: B  155 ASN cc_start: 0.7789 (t0) cc_final: 0.7374 (t0)
REVERT: B  204 CYS cc_start: 0.8072 (p) cc_final: 0.7139 (p)
REVERT: B  228 ASP cc_start: 0.7379 (m-30) cc_final: 0.6982 (m-30)
REVERT: B  230 ASN cc_start: 0.7842 (m-40) cc_final: 0.7524 (m-40)
REVERT: B  232 ILE cc_start: 0.8335 (mt) cc_final: 0.8101 (tp)
REVERT: B  246 ASP cc_start: 0.7401 (t70) cc_final: 0.7043 (t70)
REVERT: B  251 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8017 (mtt-85)
REVERT: B  283 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7237 (tpt90)
REVERT: B  293 ASN cc_start: 0.8581 (p0) cc_final: 0.8324 (p0)
REVERT: B  325 MET cc_start: 0.7316 (mpp) cc_final: 0.6734 (mpp)
REVERT: C   52 MET cc_start: 0.7993 (tpt) cc_final: 0.7440 (tpt)
REVERT: C   58 ARG cc_start: 0.6882 (mtt90) cc_final: 0.6600 (mtt90)
REVERT: C   69 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6100 (mpp)
REVERT: R  131 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: R  183 MET cc_start: 0.5087 (mtt) cc_final: 0.4244 (mtt)
REVERT: R  187 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5019 (pmm)
REVERT: R  245 ARG cc_start: 0.6185 (ptt180) cc_final: 0.5849 (ppt170)
REVERT: R  246 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6465 (tp)
REVERT: R  250 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7776 (mp)
REVERT: R  289 ASN cc_start: 0.5880 (t0) cc_final: 0.4961 (t0)
REVERT: R  293 TYR cc_start: 0.7007 (m-80) cc_final: 0.6748 (m-80)
REVERT: S   39 GLN cc_start: 0.8167 (tp40) cc_final: 0.7880 (tp40)
REVERT: S   52 SER cc_start: 0.8142 (t) cc_final: 0.7908 (p)
REVERT: S   78 THR cc_start: 0.8423 (m) cc_final: 0.7847 (t)
REVERT: S   80 PHE cc_start: 0.7746 (m-80) cc_final: 0.7288 (m-80)
REVERT: S  234 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5868 (pp20)
REVERT: D   26 HIS cc_start: 0.5893 (OUTLIER) cc_final: 0.4667 (t70)
  outliers start: 20
  outliers final: 11
  residues processed: 262
  average time/residue: 0.2479
  time to fit residues: 88.5018
Evaluate side-chains
  268 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 249
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain R residue   31 ILE
Chi-restraints excluded: chain R residue  131 ILE
Chi-restraints excluded: chain R residue  162 MET
Chi-restraints excluded: chain R residue  187 MET
Chi-restraints excluded: chain R residue  246 LEU
Chi-restraints excluded: chain R residue  250 ILE
Chi-restraints excluded: chain S residue   31 SER
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  215 THR
Chi-restraints excluded: chain S residue  233 LEU
Chi-restraints excluded: chain S residue  234 GLU
Chi-restraints excluded: chain D residue   26 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 101 optimal weight:    0.0070
   chunk 104 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.188792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.161247 restraints weight = 13500.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 2.88
r_work: 0.3862 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6734
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9289  Z= 0.160
  Angle     :  0.654   8.928  12586  Z= 0.343
  Chirality :  0.044   0.195   1421
  Planarity :  0.005   0.060   1590
  Dihedral  :  4.883  36.028   1261
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.92 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.35 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.75 (0.25), residues: 1142
  helix:  1.29 (0.27), residues: 378
  sheet: -0.15 (0.33), residues: 248
  loop : -2.11 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.029   0.001   PHE A 274 
 TYR   0.060   0.002   TYR R 114 
 ARG   0.006   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  406)
  hydrogen bonds       : angle       4.70740 ( 1161)
  SS BOND              : bond        0.00078 (    1)
  SS BOND              : angle       2.97046 (    2)
  covalent geometry    : bond        0.00361 ( 9288)
  covalent geometry    : angle       0.65333 (12584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5115.50 seconds
wall clock time: 89 minutes 41.79 seconds (5381.79 seconds total)