Starting phenix.real_space_refine
on Thu Mar 13 04:57:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ejk_31162/03_2025/7ejk_31162_neut.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.189
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5484      2.51       5
     N    1460      2.21       5
     O    1583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1699
          Classifications: {'peptide': 215}
          Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 203}
          Chain breaks: 2
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2567
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 324}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48}
    Chain: "H"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2089
          Classifications: {'peptide': 257}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 246}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'J5C': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   LYS H 236 " occ=0.00
      ... (7 atoms not shown)
      pdb=" NZ  LYS H 236 " occ=0.00
  Time building chain proxies: 5.24, per 1000 atoms: 0.61
  Number of scatterers: 8586
  At special positions: 0
  Unit cell: (90.1, 119.85, 124.95, 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      59     16.00
     O    1583      8.00
     N    1460      7.00
     C    5484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 121 " - pdb=" SG  CYS R 203 " 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: 2.19
  Conformation dependent library (CDL) restraints added in 947.3 milliseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2042

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 13 sheets defined
      35.5% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.520A  pdb=" N   PHE A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 310
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 8 through 25
    Processing helix  chain 'G' and resid 10 through 23
      removed outlier: 3.776A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU G  22 " --> pdb=" O   GLN G  18 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA G  23 " --> pdb=" O   LEU G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.582A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.809A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 208 through 212
      removed outlier: 3.700A  pdb=" N   VAL H 212 " --> pdb=" O   ALA H 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 47 through 76
      removed outlier: 3.529A  pdb=" N   SER R  76 " --> pdb=" O   ALA R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 84 through 108
      removed outlier: 4.201A  pdb=" N   ILE R 102 " --> pdb=" O   ALA R  98 " (cutoff:3.500A)
      Proline residue:  R 103  - end of helix
    Processing helix  chain 'R' and resid 117 through 151
      removed outlier: 4.180A  pdb=" N   CYS R 121 " --> pdb=" O   GLY R 117 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU R 122 " --> pdb=" O   LYS R 118 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   ILE R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA R 126 " --> pdb=" O   GLU R 122 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   SER R 135 " --> pdb=" O   PHE R 131 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE R 136 " --> pdb=" O   CYS R 132 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 158
    Processing helix  chain 'R' and resid 161 through 181
    Processing helix  chain 'R' and resid 208 through 241
      removed outlier: 4.057A  pdb=" N   SER R 214 " --> pdb=" O   TRP R 210 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ALA R 222 " --> pdb=" O   GLY R 218 " (cutoff:3.500A)
      Proline residue:  R 223  - end of helix
    Processing helix  chain 'R' and resid 382 through 414
      removed outlier: 3.697A  pdb=" N   ARG R 386 " --> pdb=" O   ASN R 382 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   VAL R 390 " --> pdb=" O   ARG R 386 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   PHE R 398 " --> pdb=" O   VAL R 394 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL R 399 " --> pdb=" O   ILE R 395 " (cutoff:3.500A)
      Proline residue:  R 404  - end of helix
      removed outlier: 3.658A  pdb=" N   ALA R 413 " --> pdb=" O   TYR R 409 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   VAL R 414 " --> pdb=" O   THR R 410 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 422 through 444
      removed outlier: 3.740A  pdb=" N   TYR R 431 " --> pdb=" O   PHE R 427 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   CYS R 432 " --> pdb=" O   TRP R 428 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ASN R 433 " --> pdb=" O   PHE R 429 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   SER R 434 " --> pdb=" O   GLY R 430 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER R 435 " --> pdb=" O   TYR R 431 " (cutoff:3.500A)
      Proline residue:  R 438  - end of helix
      removed outlier: 3.511A  pdb=" N   THR R 442 " --> pdb=" O   PRO R 438 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE R 444 " --> pdb=" O   ILE R 440 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 445 through 457
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.994A  pdb=" N   VAL A 186 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 3.817A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.061A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE B  80 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.807A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.609A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.658A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.543A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.846A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.644A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR H  69 " --> pdb=" O   GLN H  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.757A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 134 through 135
      removed outlier: 3.512A  pdb=" N   THR H 231 " --> pdb=" O   TYR H 215 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU H 162 " --> pdb=" O   TYR H 178 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   TYR H 178 " --> pdb=" O   LEU H 162 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 147 through 148
      removed outlier: 3.556A  pdb=" N   SER H 194 " --> pdb=" O   THR H 201 " (cutoff:3.500A)

    369 hydrogen bonds defined for protein.
    1050 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: 2.39

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1381
        1.31 -     1.44: 2461
        1.44 -     1.56: 4846
        1.56 -     1.69: 0
        1.69 -     1.82: 81
  Bond restraints: 8769
  Sorted by residual:
  bond pdb=" C9  J5C R 501 "
       pdb=" N13 J5C R 501 "
    ideal  model  delta    sigma   weight residual
    1.277  1.473 -0.196 2.00e-02 2.50e+03 9.65e+01
  bond pdb=" CA  ARG R 146 "
       pdb=" C   ARG R 146 "
    ideal  model  delta    sigma   weight residual
    1.524  1.455  0.069 1.24e-02 6.50e+03 3.09e+01
  bond pdb=" CA  PHE R 406 "
       pdb=" C   PHE R 406 "
    ideal  model  delta    sigma   weight residual
    1.524  1.453  0.070 1.29e-02 6.01e+03 2.98e+01
  bond pdb=" C9  J5C R 501 "
       pdb=" N10 J5C R 501 "
    ideal  model  delta    sigma   weight residual
    1.373  1.472 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" C   ARG R 146 "
       pdb=" O   ARG R 146 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.15e-02 7.56e+03 2.39e+01
  ... (remaining 8764 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 11677
        2.62 -     5.25: 160
        5.25 -     7.87: 38
        7.87 -    10.49: 3
       10.49 -    13.12: 3
  Bond angle restraints: 11881
  Sorted by residual:
  angle pdb=" N   ILE R 154 "
        pdb=" CA  ILE R 154 "
        pdb=" C   ILE R 154 "
      ideal   model   delta    sigma   weight residual
     110.53  117.54   -7.01 9.40e-01 1.13e+00 5.56e+01
  angle pdb=" N   ALA R 153 "
        pdb=" CA  ALA R 153 "
        pdb=" C   ALA R 153 "
      ideal   model   delta    sigma   weight residual
     111.28  117.87   -6.59 1.09e+00 8.42e-01 3.66e+01
  angle pdb=" C   ASP A 328 "
        pdb=" CA  ASP A 328 "
        pdb=" CB  ASP A 328 "
      ideal   model   delta    sigma   weight residual
     109.76  120.37  -10.61 1.99e+00 2.53e-01 2.84e+01
  angle pdb=" N   PHE R 405 "
        pdb=" CA  PHE R 405 "
        pdb=" C   PHE R 405 "
      ideal   model   delta    sigma   weight residual
     111.07  116.64   -5.57 1.07e+00 8.73e-01 2.71e+01
  angle pdb=" N   ARG R 146 "
        pdb=" CA  ARG R 146 "
        pdb=" C   ARG R 146 "
      ideal   model   delta    sigma   weight residual
     110.97  105.32    5.65 1.09e+00 8.42e-01 2.68e+01
  ... (remaining 11876 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 4724
       17.61 -    35.22: 390
       35.22 -    52.83: 57
       52.83 -    70.44: 10
       70.44 -    88.05: 6
  Dihedral angle restraints: 5187
    sinusoidal: 2022
      harmonic: 3165
  Sorted by residual:
  dihedral pdb=" CA  THR B  29 "
           pdb=" C   THR B  29 "
           pdb=" N   LEU B  30 "
           pdb=" CA  LEU B  30 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   26.27  -26.27     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" C   LEU A 348 "
           pdb=" N   LEU A 348 "
           pdb=" CA  LEU A 348 "
           pdb=" CB  LEU A 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.09  -10.51     0      2.50e+00 1.60e-01 1.77e+01
  dihedral pdb=" C   HIS R 446 "
           pdb=" N   HIS R 446 "
           pdb=" CA  HIS R 446 "
           pdb=" CB  HIS R 446 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.59    9.99     0      2.50e+00 1.60e-01 1.60e+01
  ... (remaining 5184 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1267
       0.103 -    0.205: 71
       0.205 -    0.308: 5
       0.308 -    0.411: 1
       0.411 -    0.514: 1
  Chirality restraints: 1345
  Sorted by residual:
  chirality pdb=" CA  HIS R 446 "
            pdb=" N   HIS R 446 "
            pdb=" C   HIS R 446 "
            pdb=" CB  HIS R 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.59e+00
  chirality pdb=" CA  SER H  85 "
            pdb=" N   SER H  85 "
            pdb=" C   SER H  85 "
            pdb=" CB  SER H  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  ALA R 153 "
            pdb=" N   ALA R 153 "
            pdb=" C   ALA R 153 "
            pdb=" CB  ALA R 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.20    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1342 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 349 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.31e+00
        pdb=" C   ARG A 349 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ARG A 349 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY A 350 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP R 402 "    0.013 2.00e-02 2.50e+03   1.06e-02 2.78e+00
        pdb=" CG  TRP R 402 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP R 402 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP R 402 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP R 402 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP R 402 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP R 402 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP R 402 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP R 402 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP R 402 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 422 "    0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   LEU R 422 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU R 422 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE R 423 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.18: 5
        2.18 -     2.86: 3289
        2.86 -     3.54: 12125
        3.54 -     4.22: 18721
        4.22 -     4.90: 33360
  Nonbonded interactions: 67500
  Sorted by model distance:
  nonbonded pdb=" O   THR R 408 "
            pdb=" O   LEU R 411 "
     model   vdw
     1.495 2.432
  nonbonded pdb=" O   LEU A 353 "
            pdb=" CD1 LEU A 353 "
     model   vdw
     1.855 3.460
  nonbonded pdb=" O   PHE R 405 "
            pdb=" OG1 THR R 408 "
     model   vdw
     2.024 3.040
  nonbonded pdb=" O   ILE B  33 "
            pdb=" OG1 THR B  34 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.166 3.040
  ... (remaining 67495 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=0.00 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.010
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
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      :  0.006   0.196   8769  Z= 0.345
  Angle     :  0.773  13.116  11881  Z= 0.477
  Chirality :  0.050   0.514   1345
  Planarity :  0.003   0.036   1497
  Dihedral  : 13.043  88.054   3136
  Min Nonbonded Distance : 1.495

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.64 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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: -0.01 (0.27), residues: 1072
  helix:  1.86 (0.30), residues: 338
  sheet: -0.02 (0.33), residues: 261
  loop : -1.41 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R 402 
 HIS   0.004   0.001   HIS R 446 
 PHE   0.024   0.001   PHE R 427 
 TYR   0.007   0.001   TYR H 178 
 ARG   0.011   0.000   ARG R 450 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 213
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8684 (t0) cc_final: 0.8393 (t0)
REVERT: A   53 MET cc_start: 0.7795 (ptp) cc_final: 0.7091 (ptm)
REVERT: B   78 LYS cc_start: 0.9029 (mttm) cc_final: 0.8786 (mmtm)
REVERT: B  215 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7578 (mp0)
REVERT: B  217 MET cc_start: 0.7694 (ppp) cc_final: 0.7398 (ppp)
REVERT: H   76 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8626 (tppp)
REVERT: H  208 GLU cc_start: 0.7826 (pt0) cc_final: 0.6203 (pt0)
REVERT: R   94 ASP cc_start: 0.7561 (m-30) cc_final: 0.7304 (m-30)
REVERT: R  175 ILE cc_start: 0.9111 (tp) cc_final: 0.8835 (mm)
REVERT: R  423 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7950 (t80)
REVERT: R  445 ASN cc_start: 0.8824 (t0) cc_final: 0.8619 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 217
  average time/residue: 0.2418
  time to fit residues: 69.1488
Evaluate side-chains
  166 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  423 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
A 256 ASN
A 305 GLN
A 331 ASN
A 347 ASN
B 239 ASN
B 268 ASN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.091808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076167 restraints weight = 24104.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.15
r_work: 0.3118 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8769  Z= 0.218
  Angle     :  0.703  15.694  11881  Z= 0.369
  Chirality :  0.045   0.172   1345
  Planarity :  0.004   0.044   1497
  Dihedral  :  4.958  52.188   1197
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.18 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.13 (0.26), residues: 1072
  helix:  1.83 (0.29), residues: 341
  sheet:  0.29 (0.32), residues: 260
  loop : -1.37 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 402 
 HIS   0.009   0.001   HIS A 189 
 PHE   0.026   0.002   PHE R 387 
 TYR   0.017   0.002   TYR R 156 
 ARG   0.008   0.001   ARG A 206 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 200
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LYS cc_start: 0.9394 (tmtt) cc_final: 0.9055 (tttt)
REVERT: A   26 ASP cc_start: 0.9035 (t0) cc_final: 0.8825 (t0)
REVERT: B   59 TYR cc_start: 0.8697 (m-80) cc_final: 0.8290 (m-80)
REVERT: B  183 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7387 (t-90)
REVERT: B  215 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7722 (mp0)
REVERT: B  217 MET cc_start: 0.8133 (ppp) cc_final: 0.7614 (ppp)
REVERT: H   42 GLU cc_start: 0.8079 (pp20) cc_final: 0.7861 (pp20)
REVERT: H   43 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8534 (mmtm)
REVERT: R  115 TYR cc_start: 0.6144 (m-80) cc_final: 0.5849 (m-80)
REVERT: R  175 ILE cc_start: 0.9177 (tp) cc_final: 0.8943 (mm)
REVERT: R  423 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7620 (t80)
REVERT: R  445 ASN cc_start: 0.8865 (t0) cc_final: 0.8565 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 209
  average time/residue: 0.2000
  time to fit residues: 57.1748
Evaluate side-chains
  183 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  394 VAL
Chi-restraints excluded: chain R residue  397 VAL
Chi-restraints excluded: chain R residue  423 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 101 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 96 optimal weight:    7.9990
   chunk 60 optimal weight:    8.9990
   chunk 95 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3450 r_free = 0.3450 target = 0.088058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072409 restraints weight = 24927.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 3.15
r_work: 0.3032 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8769  Z= 0.351
  Angle     :  0.711   9.045  11881  Z= 0.376
  Chirality :  0.046   0.166   1345
  Planarity :  0.004   0.046   1497
  Dihedral  :  5.322  53.643   1195
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.41 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.13 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.01 (0.26), residues: 1072
  helix:  1.69 (0.29), residues: 342
  sheet:  0.20 (0.32), residues: 268
  loop : -1.45 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP R 402 
 HIS   0.008   0.002   HIS A 189 
 PHE   0.024   0.002   PHE R 387 
 TYR   0.020   0.002   TYR R 235 
 ARG   0.005   0.001   ARG A 206 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 177
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
REVERT: A   20 GLU cc_start: 0.9155 (tp30) cc_final: 0.8866 (tp30)
REVERT: A   26 ASP cc_start: 0.9032 (t0) cc_final: 0.8811 (m-30)
REVERT: B   59 TYR cc_start: 0.8958 (m-80) cc_final: 0.8372 (m-80)
REVERT: B   75 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8611 (mm-40)
REVERT: B  183 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7537 (t-90)
REVERT: B  215 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7849 (mp0)
REVERT: B  285 LEU cc_start: 0.8832 (mt) cc_final: 0.8493 (mp)
REVERT: G   20 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8452 (mttt)
REVERT: H   39 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: H   42 GLU cc_start: 0.8323 (pp20) cc_final: 0.8052 (pp20)
REVERT: H   43 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8556 (mmtm)
REVERT: R  175 ILE cc_start: 0.9218 (tp) cc_final: 0.8998 (mm)
REVERT: R  402 TRP cc_start: 0.8370 (m100) cc_final: 0.8079 (m100)
REVERT: R  423 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7544 (t80)
REVERT: R  445 ASN cc_start: 0.8858 (t0) cc_final: 0.8591 (t0)
  outliers start: 28
  outliers final: 20
  residues processed: 195
  average time/residue: 0.2164
  time to fit residues: 57.3384
Evaluate side-chains
  186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 164
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  214 VAL
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  394 VAL
Chi-restraints excluded: chain R residue  397 VAL
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 76 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 29 optimal weight:    0.1980
   chunk 86 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 31 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
A 305 GLN
A 347 ASN
** B 311 HIS ** 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 = 0.3504 r_free = 0.3504 target = 0.091166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.075596 restraints weight = 24318.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.15
r_work: 0.3093 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8769  Z= 0.175
  Angle     :  0.651   9.870  11881  Z= 0.340
  Chirality :  0.044   0.167   1345
  Planarity :  0.003   0.046   1497
  Dihedral  :  5.003  53.635   1195
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.70 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.15 (0.26), residues: 1072
  helix:  1.83 (0.29), residues: 343
  sheet:  0.34 (0.32), residues: 266
  loop : -1.42 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 402 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.022   0.001   PHE R 387 
 TYR   0.016   0.001   TYR R 235 
 ARG   0.004   0.000   ARG A 206 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 195
  time to evaluate  : 0.959 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   25 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8821 (tm-30)
REVERT: A   26 ASP cc_start: 0.9045 (t0) cc_final: 0.8755 (m-30)
REVERT: A  187 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: A  244 MET cc_start: 0.7908 (mmp) cc_final: 0.7366 (mmp)
REVERT: A  246 GLU cc_start: 0.8149 (tp30) cc_final: 0.7890 (tp30)
REVERT: B   59 TYR cc_start: 0.8698 (m-80) cc_final: 0.8149 (m-80)
REVERT: B   75 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8427 (mm-40)
REVERT: B  183 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7415 (t-90)
REVERT: B  215 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7649 (mp0)
REVERT: B  285 LEU cc_start: 0.8810 (mt) cc_final: 0.8388 (mp)
REVERT: G   20 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8477 (mttt)
REVERT: H   39 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: H   42 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7959 (pp20)
REVERT: H   93 MET cc_start: 0.8528 (tpp) cc_final: 0.8312 (tpp)
REVERT: R  115 TYR cc_start: 0.6129 (m-80) cc_final: 0.5792 (m-80)
REVERT: R  175 ILE cc_start: 0.9243 (tp) cc_final: 0.9007 (mm)
REVERT: R  423 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7583 (t80)
REVERT: R  445 ASN cc_start: 0.8771 (t0) cc_final: 0.8529 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 204
  average time/residue: 0.2046
  time to fit residues: 57.1191
Evaluate side-chains
  190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 88 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3474 r_free = 0.3474 target = 0.089514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.073978 restraints weight = 24526.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.14
r_work: 0.3066 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8769  Z= 0.238
  Angle     :  0.674   8.895  11881  Z= 0.353
  Chirality :  0.044   0.155   1345
  Planarity :  0.004   0.046   1497
  Dihedral  :  5.081  55.010   1195
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.13 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.27 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.08 (0.26), residues: 1072
  helix:  1.74 (0.29), residues: 347
  sheet:  0.32 (0.33), residues: 267
  loop : -1.47 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP R 402 
 HIS   0.008   0.001   HIS A 189 
 PHE   0.022   0.001   PHE R 387 
 TYR   0.018   0.001   TYR R 235 
 ARG   0.002   0.000   ARG H  98 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.946 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
REVERT: A   26 ASP cc_start: 0.9033 (t0) cc_final: 0.8785 (m-30)
REVERT: A  244 MET cc_start: 0.8019 (mmp) cc_final: 0.7399 (mmp)
REVERT: B   59 TYR cc_start: 0.8877 (m-80) cc_final: 0.8395 (m-80)
REVERT: B  183 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7462 (t-90)
REVERT: B  215 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7653 (mp0)
REVERT: B  285 LEU cc_start: 0.8864 (mt) cc_final: 0.8496 (mp)
REVERT: G   20 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8481 (mttt)
REVERT: G   25 ILE cc_start: 0.6489 (mp) cc_final: 0.6285 (mt)
REVERT: H    3 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.8016 (pp30)
REVERT: H   39 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: H   42 GLU cc_start: 0.8388 (pp20) cc_final: 0.7654 (pp20)
REVERT: H   43 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8245 (mmtm)
REVERT: H   91 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8168 (t)
REVERT: H   93 MET cc_start: 0.8610 (tpp) cc_final: 0.8377 (tpp)
REVERT: H  148 ARG cc_start: 0.6738 (tpp80) cc_final: 0.6527 (tpp80)
REVERT: H  208 GLU cc_start: 0.8507 (pt0) cc_final: 0.8302 (pt0)
REVERT: R  152 GLN cc_start: 0.8216 (mp10) cc_final: 0.7855 (mp10)
REVERT: R  160 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7629 (mmt90)
REVERT: R  175 ILE cc_start: 0.9246 (tp) cc_final: 0.9039 (mm)
REVERT: R  423 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7657 (t80)
REVERT: R  445 ASN cc_start: 0.8766 (t0) cc_final: 0.8533 (t0)
  outliers start: 34
  outliers final: 20
  residues processed: 197
  average time/residue: 0.1945
  time to fit residues: 52.9538
Evaluate side-chains
  194 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3452 r_free = 0.3452 target = 0.088209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.072722 restraints weight = 24489.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 3.12
r_work: 0.3038 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8769  Z= 0.302
  Angle     :  0.695   9.396  11881  Z= 0.365
  Chirality :  0.044   0.151   1345
  Planarity :  0.004   0.047   1497
  Dihedral  :  5.245  56.478   1195
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.04 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 19.02 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.02 (0.26), residues: 1072
  helix:  1.69 (0.28), residues: 348
  sheet:  0.29 (0.33), residues: 264
  loop : -1.51 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP R 402 
 HIS   0.007   0.001   HIS A 189 
 PHE   0.021   0.001   PHE R 387 
 TYR   0.018   0.001   TYR R 235 
 ARG   0.003   0.000   ARG B 283 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 173
  time to evaluate  : 0.937 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9283 (t0) cc_final: 0.8996 (t0)
REVERT: A  206 ARG cc_start: 0.8869 (mmp80) cc_final: 0.8602 (mmp80)
REVERT: A  244 MET cc_start: 0.8070 (mmp) cc_final: 0.7355 (mmp)
REVERT: B   59 TYR cc_start: 0.9009 (m-80) cc_final: 0.8381 (m-80)
REVERT: B   75 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8415 (mm-40)
REVERT: B  183 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7495 (t-90)
REVERT: B  215 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7785 (mp0)
REVERT: G   20 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8466 (mttt)
REVERT: H    3 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7998 (pp30)
REVERT: H   39 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8004 (tm-30)
REVERT: H   42 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7452 (pp20)
REVERT: H   43 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8068 (mmtm)
REVERT: H   93 MET cc_start: 0.8669 (tpp) cc_final: 0.8424 (tpp)
REVERT: H  208 GLU cc_start: 0.8442 (pt0) cc_final: 0.7858 (pt0)
REVERT: R   60 LEU cc_start: 0.8995 (mt) cc_final: 0.8566 (tt)
REVERT: R  239 LYS cc_start: 0.8891 (tptt) cc_final: 0.8522 (mmtt)
REVERT: R  423 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7690 (t80)
REVERT: R  445 ASN cc_start: 0.8804 (t0) cc_final: 0.8590 (t0)
  outliers start: 41
  outliers final: 25
  residues processed: 197
  average time/residue: 0.1924
  time to fit residues: 53.2153
Evaluate side-chains
  196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 167
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  218 MET
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  394 VAL
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3477 r_free = 0.3477 target = 0.089586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.074082 restraints weight = 24470.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 3.15
r_work: 0.3066 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8769  Z= 0.209
  Angle     :  0.689   9.688  11881  Z= 0.357
  Chirality :  0.044   0.222   1345
  Planarity :  0.003   0.047   1497
  Dihedral  :  5.140  57.031   1195
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.76 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.66 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.14 (0.26), residues: 1072
  helix:  1.80 (0.28), residues: 346
  sheet:  0.40 (0.32), residues: 278
  loop : -1.53 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP R 402 
 HIS   0.019   0.002   HIS A 189 
 PHE   0.020   0.001   PHE R 387 
 TYR   0.017   0.001   TYR R 235 
 ARG   0.002   0.000   ARG H  98 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 176
  time to evaluate  : 0.925 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9304 (t0) cc_final: 0.9006 (t0)
REVERT: A  206 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8557 (mmp80)
REVERT: B   59 TYR cc_start: 0.8934 (m-80) cc_final: 0.8334 (m-80)
REVERT: B   75 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8435 (mm-40)
REVERT: B  183 HIS cc_start: 0.7887 (OUTLIER) cc_final: 0.7490 (t-90)
REVERT: B  215 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7768 (mp0)
REVERT: G   20 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8488 (mttt)
REVERT: G   48 ASP cc_start: 0.8729 (p0) cc_final: 0.8474 (p0)
REVERT: H    3 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8016 (pp30)
REVERT: H   39 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8021 (tm-30)
REVERT: H   42 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7525 (pp20)
REVERT: H   43 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8081 (mmtm)
REVERT: H   91 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8196 (t)
REVERT: H   93 MET cc_start: 0.8634 (tpp) cc_final: 0.8404 (tpp)
REVERT: R   60 LEU cc_start: 0.8979 (mt) cc_final: 0.8572 (tt)
REVERT: R  152 GLN cc_start: 0.8184 (mp10) cc_final: 0.7964 (mp10)
REVERT: R  160 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.7524 (mmt90)
REVERT: R  423 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7702 (t80)
REVERT: R  445 ASN cc_start: 0.8797 (t0) cc_final: 0.8584 (t0)
  outliers start: 33
  outliers final: 23
  residues processed: 193
  average time/residue: 0.2057
  time to fit residues: 54.6640
Evaluate side-chains
  197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain H residue  218 MET
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 62 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3441 r_free = 0.3441 target = 0.087544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.072177 restraints weight = 24942.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.13
r_work: 0.3026 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8769  Z= 0.329
  Angle     :  0.740   9.764  11881  Z= 0.387
  Chirality :  0.045   0.186   1345
  Planarity :  0.004   0.048   1497
  Dihedral  :  5.360  58.835   1195
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.22 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.66 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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: -0.01 (0.26), residues: 1072
  helix:  1.65 (0.28), residues: 346
  sheet:  0.28 (0.32), residues: 280
  loop : -1.57 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP R 402 
 HIS   0.012   0.001   HIS A 189 
 PHE   0.021   0.002   PHE R 387 
 TYR   0.018   0.002   TYR R 235 
 ARG   0.005   0.000   ARG H  98 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 167
  time to evaluate  : 1.110 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9315 (t0) cc_final: 0.9035 (t0)
REVERT: A  206 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8583 (mmp80)
REVERT: B   59 TYR cc_start: 0.9039 (m-80) cc_final: 0.8414 (m-80)
REVERT: B   75 GLN cc_start: 0.8843 (mm-40) cc_final: 0.8516 (mm-40)
REVERT: B  183 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7523 (t-90)
REVERT: B  215 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7747 (mp0)
REVERT: B  225 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8374 (t70)
REVERT: G   20 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8452 (mttt)
REVERT: G   48 ASP cc_start: 0.8734 (p0) cc_final: 0.8473 (p0)
REVERT: H    3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8048 (pp30)
REVERT: H   39 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: H   42 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8181 (pp20)
REVERT: R   60 LEU cc_start: 0.8997 (mt) cc_final: 0.8570 (tt)
REVERT: R  239 LYS cc_start: 0.8900 (tptt) cc_final: 0.8543 (mmtt)
REVERT: R  423 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7693 (t80)
REVERT: R  445 ASN cc_start: 0.8824 (t0) cc_final: 0.8612 (t0)
  outliers start: 39
  outliers final: 30
  residues processed: 191
  average time/residue: 0.2061
  time to fit residues: 54.9230
Evaluate side-chains
  200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  297 TYR
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  311 HIS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  228 ILE
Chi-restraints excluded: chain R residue  397 VAL
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 42 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0570
   chunk 10 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0040
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6712

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.090532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.075066 restraints weight = 24468.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 3.16
r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.3022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8769  Z= 0.198
  Angle     :  0.723  11.335  11881  Z= 0.374
  Chirality :  0.045   0.189   1345
  Planarity :  0.004   0.048   1497
  Dihedral  :  5.192  59.290   1195
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.94 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.73 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.16 (0.26), residues: 1072
  helix:  1.82 (0.29), residues: 344
  sheet:  0.26 (0.31), residues: 287
  loop : -1.41 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP R 402 
 HIS   0.025   0.002   HIS A 189 
 PHE   0.020   0.001   PHE A 190 
 TYR   0.017   0.001   TYR R 235 
 ARG   0.006   0.000   ARG H 148 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 0.981 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9315 (t0) cc_final: 0.9031 (t0)
REVERT: B   59 TYR cc_start: 0.8860 (m-80) cc_final: 0.8361 (m-80)
REVERT: B   75 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8486 (mm-40)
REVERT: B  183 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7484 (t-90)
REVERT: B  225 HIS cc_start: 0.8658 (OUTLIER) cc_final: 0.8292 (t70)
REVERT: G   20 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8483 (mttt)
REVERT: G   48 ASP cc_start: 0.8694 (p0) cc_final: 0.8389 (p0)
REVERT: H    3 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8049 (pp30)
REVERT: H   39 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: H   42 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7620 (pp20)
REVERT: H   43 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8211 (mmtm)
REVERT: H   91 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8164 (t)
REVERT: H  148 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7104 (ttm170)
REVERT: R   60 LEU cc_start: 0.8957 (mt) cc_final: 0.8554 (tt)
REVERT: R  239 LYS cc_start: 0.8871 (tptt) cc_final: 0.8512 (mmtt)
REVERT: R  423 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7699 (t80)
REVERT: R  445 ASN cc_start: 0.8822 (t0) cc_final: 0.8620 (t0)
  outliers start: 29
  outliers final: 22
  residues processed: 200
  average time/residue: 0.1998
  time to fit residues: 55.0477
Evaluate side-chains
  198 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  297 TYR
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  143 SER
Chi-restraints excluded: chain R residue  145 ASP
Chi-restraints excluded: chain R residue  423 PHE
Chi-restraints excluded: chain R residue  447 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 25 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0060
   chunk 86 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0670
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.091375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.075904 restraints weight = 24321.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.16
r_work: 0.3103 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8769  Z= 0.195
  Angle     :  0.719  10.415  11881  Z= 0.373
  Chirality :  0.045   0.178   1345
  Planarity :  0.004   0.048   1497
  Dihedral  :  5.125  59.720   1195
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.32 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.58 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    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:  0.21 (0.26), residues: 1072
  helix:  1.81 (0.28), residues: 345
  sheet:  0.41 (0.32), residues: 282
  loop : -1.44 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP R 402 
 HIS   0.025   0.002   HIS A 189 
 PHE   0.021   0.001   PHE A 190 
 TYR   0.027   0.001   TYR R 156 
 ARG   0.008   0.000   ARG A 206 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.993 
Fit side-chains
TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.9311 (t0) cc_final: 0.9027 (t0)
REVERT: B   59 TYR cc_start: 0.8839 (m-80) cc_final: 0.8380 (m-80)
REVERT: B   75 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8416 (mm-40)
REVERT: B  183 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7433 (t-90)
REVERT: B  225 HIS cc_start: 0.8576 (OUTLIER) cc_final: 0.8187 (t70)
REVERT: G   48 ASP cc_start: 0.8662 (p0) cc_final: 0.8349 (p0)
REVERT: H   39 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: H   42 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7584 (pp20)
REVERT: H   43 LYS cc_start: 0.8714 (mmtm) cc_final: 0.8289 (mmtm)
REVERT: H   91 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8145 (t)
REVERT: H  148 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7071 (ttm170)
REVERT: R   60 LEU cc_start: 0.8932 (mt) cc_final: 0.8529 (tt)
REVERT: R  239 LYS cc_start: 0.8856 (tptt) cc_final: 0.8512 (mmtt)
REVERT: R  423 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: R  445 ASN cc_start: 0.8811 (t0) cc_final: 0.8604 (t0)
  outliers start: 26
  outliers final: 17
  residues processed: 197
  average time/residue: 0.2478
  time to fit residues: 67.4636
Evaluate side-chains
  193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 LEU
Chi-restraints excluded: chain A residue  189 HIS
Chi-restraints excluded: chain A residue  217 GLU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  250 CYS
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain G residue   52 THR
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   42 GLU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   84 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain R residue   74 PHE
Chi-restraints excluded: chain R residue  110 VAL
Chi-restraints excluded: chain R residue  423 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    0.1980
   chunk 94 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 189 HIS
A 205 GLN
** B 311 HIS ** 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 = 0.3496 r_free = 0.3496 target = 0.090842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.075192 restraints weight = 24631.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 3.23
r_work: 0.3099 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8769  Z= 0.215
  Angle     :  0.731  10.171  11881  Z= 0.378
  Chirality :  0.045   0.183   1345
  Planarity :  0.004   0.068   1497
  Dihedral  :  5.109  58.895   1195
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.50 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.22 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.33 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1072
  helix:  1.78 (0.28), residues: 346
  sheet:  0.40 (0.32), residues: 280
  loop : -1.46 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.027   0.002   HIS A 189 
 PHE   0.020   0.001   PHE R 387 
 TYR   0.021   0.001   TYR R 156 
 ARG   0.014   0.001   ARG A 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4109.86 seconds
wall clock time: 72 minutes 15.54 seconds (4335.54 seconds total)