Starting phenix.real_space_refine
on Thu Mar 13 03:32:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vuz_32132/03_2025/7vuz_32132.cif"
  }
  resolution = 2.89
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    5493      2.51       5
     N    1439      2.21       5
     O    1588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 71 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8584
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 1995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1995
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1750
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2598
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 427
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1786
          Classifications: {'peptide': 233}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.34, per 1000 atoms: 0.62
  Number of scatterers: 8584
  At special positions: 0
  Unit cell: (116.833, 114.347, 100.261, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1588      8.00
     N    1439      7.00
     C    5493      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.06
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " 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: 2.00
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2038

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 14 sheets defined
      36.4% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'R' and resid 36 through 57
      removed outlier: 3.521A  pdb=" N   LEU R  42 " --> pdb=" O   LEU R  38 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   VAL R  43 " --> pdb=" O   PHE R  39 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL R  46 " --> pdb=" O   LEU R  42 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   PHE R  50 " --> pdb=" O   VAL R  46 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY R  56 " --> pdb=" O   LEU R  52 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE R  57 " --> pdb=" O   TRP R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 95
    Processing helix  chain 'R' and resid 103 through 133
      removed outlier: 4.282A  pdb=" N   THR R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   VAL R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 168
    Processing helix  chain 'R' and resid 179 through 212
      removed outlier: 3.946A  pdb=" N   PHE R 183 " --> pdb=" O   TRP R 179 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY R 212 " --> pdb=" O   ARG R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 235
    Processing helix  chain 'R' and resid 236 through 245
      removed outlier: 3.861A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 251
      removed outlier: 3.658A  pdb=" N   LYS R 251 " --> pdb=" O   LEU R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 253 through 260
      removed outlier: 3.715A  pdb=" N   HIS R 259 " --> pdb=" O   VAL R 255 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 279
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 208 through 214
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.580A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.965A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.568A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 4.034A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 25
    Processing helix  chain 'B' and resid 29 through 37
      removed outlier: 4.927A  pdb=" N   ASN B  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN B  36 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.730A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.532A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.187A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.680A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.680A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.667A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.858A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.965A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.154A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151
      removed outlier: 3.876A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.706A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.708A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.909A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 129 through 130
      removed outlier: 3.899A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER S 194 " --> pdb=" O   THR S 201 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.895A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR S 231 " --> pdb=" O   TYR S 215 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TYR S 216 " --> pdb=" O   PHE S 165 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET S 218 " --> pdb=" O   TYR S 163 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU S 166 " --> pdb=" O   GLN S 174 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1188 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: 2.43

  Time building geometry restraints manager: 2.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2523
        1.34 -     1.46: 2378
        1.46 -     1.59: 3780
        1.59 -     1.72: 1
        1.72 -     1.85: 89
  Bond restraints: 8771
  Sorted by residual:
  bond pdb=" C   PRO R 238 "
       pdb=" N   PHE R 239 "
    ideal  model  delta    sigma   weight residual
    1.335  1.471 -0.137 1.31e-02 5.83e+03 1.09e+02
  bond pdb=" C   GLY R 236 "
       pdb=" N   LEU R 237 "
    ideal  model  delta    sigma   weight residual
    1.331  1.440 -0.109 2.07e-02 2.33e+03 2.77e+01
  bond pdb=" C17 CLR R 401 "
       pdb=" C20 CLR R 401 "
    ideal  model  delta    sigma   weight residual
    1.535  1.626 -0.091 2.00e-02 2.50e+03 2.06e+01
  bond pdb=" C   LEU R 237 "
       pdb=" N   PRO R 238 "
    ideal  model  delta    sigma   weight residual
    1.336  1.372 -0.036 1.20e-02 6.94e+03 9.25e+00
  bond pdb=" CG  LEU B 146 "
       pdb=" CD2 LEU B 146 "
    ideal  model  delta    sigma   weight residual
    1.521  1.422  0.099 3.30e-02 9.18e+02 8.99e+00
  ... (remaining 8766 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.08: 11385
        3.08 -     6.15: 414
        6.15 -     9.23: 64
        9.23 -    12.31: 22
       12.31 -    15.38: 3
  Bond angle restraints: 11888
  Sorted by residual:
  angle pdb=" N   ASP R 254 "
        pdb=" CA  ASP R 254 "
        pdb=" C   ASP R 254 "
      ideal   model   delta    sigma   weight residual
     111.28  120.50   -9.22 1.09e+00 8.42e-01 7.16e+01
  angle pdb=" C   ASN R 275 "
        pdb=" N   PRO R 276 "
        pdb=" CA  PRO R 276 "
      ideal   model   delta    sigma   weight residual
     119.47  111.39    8.08 1.16e+00 7.43e-01 4.86e+01
  angle pdb=" CA  PRO R 276 "
        pdb=" N   PRO R 276 "
        pdb=" CD  PRO R 276 "
      ideal   model   delta    sigma   weight residual
     112.00  102.58    9.42 1.40e+00 5.10e-01 4.53e+01
  angle pdb=" N   GLN B  17 "
        pdb=" CA  GLN B  17 "
        pdb=" CB  GLN B  17 "
      ideal   model   delta    sigma   weight residual
     110.16  119.85   -9.69 1.48e+00 4.57e-01 4.29e+01
  angle pdb=" N   PRO R 276 "
        pdb=" CA  PRO R 276 "
        pdb=" C   PRO R 276 "
      ideal   model   delta    sigma   weight residual
     113.81  123.17   -9.36 1.45e+00 4.76e-01 4.17e+01
  ... (remaining 11883 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.51: 4518
       14.51 -    29.02: 538
       29.02 -    43.54: 128
       43.54 -    58.05: 18
       58.05 -    72.56: 10
  Dihedral angle restraints: 5212
    sinusoidal: 2050
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CA  PHE R 172 "
           pdb=" C   PHE R 172 "
           pdb=" N   SER R 173 "
           pdb=" CA  SER R 173 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.80  -42.20     0      5.00e+00 4.00e-02 7.12e+01
  dihedral pdb=" CA  GLY B 185 "
           pdb=" C   GLY B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.37   29.63     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.85   29.15     0      5.00e+00 4.00e-02 3.40e+01
  ... (remaining 5209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1212
       0.122 -    0.244: 124
       0.244 -    0.366: 13
       0.366 -    0.488: 2
       0.488 -    0.610: 3
  Chirality restraints: 1354
  Sorted by residual:
  chirality pdb=" CA  PRO R 276 "
            pdb=" N   PRO R 276 "
            pdb=" C   PRO R 276 "
            pdb=" CB  PRO R 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.11    0.61 2.00e-01 2.50e+01 9.30e+00
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.02   -0.61 2.00e-01 2.50e+01 9.30e+00
  chirality pdb=" CB  VAL B 296 "
            pdb=" CA  VAL B 296 "
            pdb=" CG1 VAL B 296 "
            pdb=" CG2 VAL B 296 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.08   -0.55 2.00e-01 2.50e+01 7.54e+00
  ... (remaining 1351 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 275 "    0.134 5.00e-02 4.00e+02   2.01e-01 6.47e+01
        pdb=" N   PRO R 276 "   -0.348 5.00e-02 4.00e+02
        pdb=" CA  PRO R 276 "    0.104 5.00e-02 4.00e+02
        pdb=" CD  PRO R 276 "    0.110 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER R 273 "    0.020 2.00e-02 2.50e+03   4.12e-02 1.70e+01
        pdb=" C   SER R 273 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   SER R 273 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ALA R 274 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 230 "   -0.016 2.00e-02 2.50e+03   2.66e-02 1.41e+01
        pdb=" CG  TYR A 230 "    0.064 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 230 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 230 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 230 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 230 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 230 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 230 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 88
        2.61 -     3.18: 6696
        3.18 -     3.75: 13745
        3.75 -     4.33: 18610
        4.33 -     4.90: 31109
  Nonbonded interactions: 70248
  Sorted by model distance:
  nonbonded pdb=" O   CYS R 258 "
            pdb=" CD  PRO R 262 "
     model   vdw
     2.035 3.440
  nonbonded pdb=" OD1 ASN R  48 "
            pdb=" CG  PRO R 276 "
     model   vdw
     2.170 3.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.295 3.040
  ... (remaining 70243 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.100
  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:11.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
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      :  0.010   0.137   8771  Z= 0.654
  Angle     :  1.395  15.384  11888  Z= 0.754
  Chirality :  0.082   0.610   1354
  Planarity :  0.010   0.201   1489
  Dihedral  : 13.540  72.560   3162
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  1.28 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.89 (0.23), residues: 1081
  helix: -2.11 (0.22), residues: 355
  sheet: -1.33 (0.30), residues: 276
  loop : -1.94 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.004   TRP R 133 
 HIS   0.026   0.004   HIS S 220 
 PHE   0.035   0.004   PHE R  50 
 TYR   0.064   0.005   TYR A 230 
 ARG   0.032   0.002   ARG S  98 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 203
  time to evaluate  : 0.962 
Fit side-chains
REVERT: R  234 LEU cc_start: 0.8434 (mt) cc_final: 0.8093 (mp)
REVERT: R  252 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6710 (m-30)
REVERT: A  294 ASN cc_start: 0.6673 (m110) cc_final: 0.6360 (t0)
REVERT: A  318 GLU cc_start: 0.6400 (tp30) cc_final: 0.6000 (tp30)
REVERT: S  206 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7145 (mmp80)
  outliers start: 13
  outliers final: 4
  residues processed: 214
  average time/residue: 1.2467
  time to fit residues: 283.2331
Evaluate side-chains
  153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  252 ASP
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  271 ASN
Chi-restraints excluded: chain R residue  276 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 97 optimal weight:   30.0000
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
R  82 GLN
R 275 ASN
A  52 GLN
A 331 ASN
** B  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 HIS
B 259 GLN
B 268 ASN
S  39 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.197167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.156611 restraints weight = 10545.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 2.94
r_work: 0.4047 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8771  Z= 0.193
  Angle     :  0.696   8.689  11888  Z= 0.358
  Chirality :  0.046   0.346   1354
  Planarity :  0.005   0.053   1489
  Dihedral  :  6.872  72.766   1254
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.42 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.24), residues: 1081
  helix: -0.17 (0.26), residues: 360
  sheet: -1.10 (0.30), residues: 266
  loop : -1.58 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 213 
 PHE   0.011   0.001   PHE S  29 
 TYR   0.014   0.001   TYR A 296 
 ARG   0.011   0.001   ARG A  21 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 182
  time to evaluate  : 0.849 
Fit side-chains
REVERT: R  196 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (ttp)
REVERT: R  199 CYS cc_start: 0.7010 (p) cc_final: 0.6789 (m)
REVERT: A  318 GLU cc_start: 0.6304 (tp30) cc_final: 0.5802 (tp30)
REVERT: B   19 ARG cc_start: 0.7414 (mtm110) cc_final: 0.7063 (ttp-170)
REVERT: B   75 GLN cc_start: 0.7413 (tt0) cc_final: 0.7120 (tt0)
REVERT: G   37 LEU cc_start: 0.7701 (mm) cc_final: 0.7497 (mm)
REVERT: S  163 TYR cc_start: 0.5947 (m-80) cc_final: 0.5698 (m-80)
REVERT: S  206 ARG cc_start: 0.7539 (mmt-90) cc_final: 0.7241 (tpp-160)
  outliers start: 30
  outliers final: 7
  residues processed: 196
  average time/residue: 1.0619
  time to fit residues: 223.1609
Evaluate side-chains
  162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  196 MET
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain S residue  222 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0980
   chunk 76 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 101 optimal weight:    0.3980
   chunk 80 optimal weight:    6.9990
   chunk 42 optimal weight:    0.4980
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
A 304 GLN
A 331 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 311 HIS
B 340 ASN
G  59 ASN
** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 182 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.199832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.159887 restraints weight = 10663.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 2.97
r_work: 0.4096 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8771  Z= 0.169
  Angle     :  0.643   8.974  11888  Z= 0.325
  Chirality :  0.044   0.328   1354
  Planarity :  0.004   0.042   1489
  Dihedral  :  6.156  73.803   1246
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.63 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.85 (0.25), residues: 1081
  helix:  0.66 (0.27), residues: 365
  sheet: -0.82 (0.31), residues: 264
  loop : -1.34 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.011   0.001   PHE R  35 
 TYR   0.024   0.001   TYR A 230 
 ARG   0.005   0.000   ARG A  21 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 180
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  196 MET cc_start: 0.8445 (ttm) cc_final: 0.8221 (ttp)
REVERT: R  199 CYS cc_start: 0.6915 (p) cc_final: 0.6702 (m)
REVERT: A   25 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6482 (tp30)
REVERT: A  305 CYS cc_start: 0.7931 (m) cc_final: 0.7428 (m)
REVERT: A  318 GLU cc_start: 0.6340 (tp30) cc_final: 0.5888 (tp30)
REVERT: B   19 ARG cc_start: 0.7383 (mtm110) cc_final: 0.7059 (ttp80)
REVERT: B  215 GLU cc_start: 0.7987 (pp20) cc_final: 0.7727 (pp20)
REVERT: B  219 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7688 (ttm110)
REVERT: S  206 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7280 (tpp-160)
REVERT: S  234 GLU cc_start: 0.5899 (pm20) cc_final: 0.5665 (pm20)
  outliers start: 35
  outliers final: 15
  residues processed: 196
  average time/residue: 1.1024
  time to fit residues: 231.5107
Evaluate side-chains
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   20 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0070
   chunk 76 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 95 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.198759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.158270 restraints weight = 10599.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.4285 rms_B_bonded: 2.96
r_work: 0.4167 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8771  Z= 0.186
  Angle     :  0.645   9.737  11888  Z= 0.324
  Chirality :  0.044   0.333   1354
  Planarity :  0.003   0.037   1489
  Dihedral  :  5.987  75.355   1246
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.23 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.45 (0.26), residues: 1081
  helix:  1.11 (0.27), residues: 362
  sheet: -0.64 (0.32), residues: 261
  loop : -1.19 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.013   0.001   PHE R 104 
 TYR   0.010   0.001   TYR S 223 
 ARG   0.005   0.000   ARG A 313 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  196 MET cc_start: 0.8458 (ttm) cc_final: 0.8227 (ttp)
REVERT: R  199 CYS cc_start: 0.7012 (p) cc_final: 0.6707 (m)
REVERT: R  243 TRP cc_start: 0.6625 (t-100) cc_final: 0.5827 (t-100)
REVERT: A   25 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6611 (tp30)
REVERT: A   33 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6399 (mp0)
REVERT: A   53 MET cc_start: 0.7966 (mpt) cc_final: 0.7382 (mpt)
REVERT: A  230 TYR cc_start: 0.7280 (p90) cc_final: 0.6923 (p90)
REVERT: A  232 LEU cc_start: 0.7530 (tt) cc_final: 0.7178 (pp)
REVERT: A  241 ASN cc_start: 0.7869 (m-40) cc_final: 0.7479 (t0)
REVERT: A  296 TYR cc_start: 0.7030 (p90) cc_final: 0.6690 (p90)
REVERT: A  297 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7572 (mm-30)
REVERT: A  305 CYS cc_start: 0.8046 (m) cc_final: 0.7514 (m)
REVERT: B   15 LYS cc_start: 0.7291 (mmmt) cc_final: 0.6977 (tppp)
REVERT: B   19 ARG cc_start: 0.7313 (mtm110) cc_final: 0.7037 (ttp80)
REVERT: B  189 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6875 (t)
REVERT: B  219 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7736 (ttm110)
REVERT: B  256 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7908 (ttp80)
  outliers start: 33
  outliers final: 17
  residues processed: 188
  average time/residue: 1.1106
  time to fit residues: 222.9811
Evaluate side-chains
  177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0970
   chunk 49 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.191669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.150362 restraints weight = 10735.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.4115 rms_B_bonded: 2.95
r_work: 0.3987 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7056
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8771  Z= 0.295
  Angle     :  0.702  11.142  11888  Z= 0.355
  Chirality :  0.047   0.340   1354
  Planarity :  0.004   0.046   1489
  Dihedral  :  6.091  76.903   1246
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.09 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.26), residues: 1081
  helix:  1.08 (0.27), residues: 367
  sheet: -0.78 (0.31), residues: 272
  loop : -1.16 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.009   0.002   HIS S 155 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.016   0.002   TYR S  59 
 ARG   0.005   0.000   ARG A 313 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 158
  time to evaluate  : 0.874 
Fit side-chains
REVERT: R  199 CYS cc_start: 0.6972 (p) cc_final: 0.6616 (m)
REVERT: R  243 TRP cc_start: 0.6595 (t-100) cc_final: 0.5784 (t-100)
REVERT: A   25 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6510 (tp30)
REVERT: A   33 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6498 (mp0)
REVERT: A   53 MET cc_start: 0.7888 (mpt) cc_final: 0.7314 (mpt)
REVERT: A  241 ASN cc_start: 0.7843 (m-40) cc_final: 0.7352 (t0)
REVERT: A  296 TYR cc_start: 0.7070 (p90) cc_final: 0.6744 (p90)
REVERT: A  297 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7479 (mm-30)
REVERT: A  305 CYS cc_start: 0.8039 (m) cc_final: 0.7520 (m)
REVERT: A  318 GLU cc_start: 0.6415 (mm-30) cc_final: 0.6049 (tp30)
REVERT: B   15 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6881 (tppp)
REVERT: B   19 ARG cc_start: 0.7272 (mtm110) cc_final: 0.7023 (ttp80)
REVERT: B   82 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7404 (m-10)
REVERT: B  189 SER cc_start: 0.7405 (OUTLIER) cc_final: 0.7026 (t)
REVERT: B  304 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (mmm-85)
REVERT: S  206 ARG cc_start: 0.6905 (tpp-160) cc_final: 0.6631 (tpp-160)
  outliers start: 42
  outliers final: 18
  residues processed: 183
  average time/residue: 1.0211
  time to fit residues: 200.9944
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  256 LEU
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 8 optimal weight:    8.9990
   chunk 39 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 23 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 80 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.189962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.148558 restraints weight = 10703.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 2.94
r_work: 0.3973 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8771  Z= 0.328
  Angle     :  0.733  10.982  11888  Z= 0.371
  Chirality :  0.048   0.341   1354
  Planarity :  0.004   0.047   1489
  Dihedral  :  6.159  76.399   1245
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 22.12 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.26), residues: 1081
  helix:  1.03 (0.27), residues: 367
  sheet: -0.89 (0.31), residues: 273
  loop : -1.21 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  82 
 HIS   0.009   0.001   HIS S 155 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.016   0.002   TYR S 223 
 ARG   0.009   0.000   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 0.856 
Fit side-chains
REVERT: R  199 CYS cc_start: 0.7027 (p) cc_final: 0.6620 (m)
REVERT: R  243 TRP cc_start: 0.6657 (t-100) cc_final: 0.5917 (t-100)
REVERT: A   25 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6577 (tp30)
REVERT: A   33 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6484 (mp0)
REVERT: A   53 MET cc_start: 0.7895 (mpt) cc_final: 0.7300 (mpt)
REVERT: A  241 ASN cc_start: 0.7703 (m-40) cc_final: 0.7263 (t0)
REVERT: A  305 CYS cc_start: 0.8086 (m) cc_final: 0.7573 (m)
REVERT: A  318 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6119 (tp30)
REVERT: B    4 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4598 (tt)
REVERT: B   15 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6871 (tppp)
REVERT: B   19 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6821 (ttp80)
REVERT: B   82 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.7381 (m-10)
REVERT: B  101 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8478 (ptp)
REVERT: B  189 SER cc_start: 0.7554 (OUTLIER) cc_final: 0.7190 (t)
REVERT: S  206 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.6701 (tpp-160)
REVERT: S  234 GLU cc_start: 0.6108 (pm20) cc_final: 0.5853 (pm20)
  outliers start: 41
  outliers final: 21
  residues processed: 176
  average time/residue: 1.0354
  time to fit residues: 196.4427
Evaluate side-chains
  173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   38 LEU
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   82 TRP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.194046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.153044 restraints weight = 10714.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.4155 rms_B_bonded: 2.94
r_work: 0.4028 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8771  Z= 0.212
  Angle     :  0.692   9.931  11888  Z= 0.348
  Chirality :  0.045   0.337   1354
  Planarity :  0.003   0.038   1489
  Dihedral  :  5.955  76.394   1245
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.82 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.26), residues: 1081
  helix:  1.24 (0.28), residues: 366
  sheet: -0.78 (0.31), residues: 266
  loop : -1.14 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.011   0.001   PHE R 232 
 TYR   0.016   0.001   TYR S 223 
 ARG   0.006   0.000   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: R  199 CYS cc_start: 0.7024 (p) cc_final: 0.6586 (m)
REVERT: R  243 TRP cc_start: 0.6684 (t-100) cc_final: 0.6218 (t-100)
REVERT: A   25 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6552 (tp30)
REVERT: A   33 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6171 (mp0)
REVERT: A   53 MET cc_start: 0.7860 (mpt) cc_final: 0.7311 (mpt)
REVERT: A  230 TYR cc_start: 0.7365 (p90) cc_final: 0.6956 (p90)
REVERT: A  232 LEU cc_start: 0.7569 (tt) cc_final: 0.7306 (pp)
REVERT: A  241 ASN cc_start: 0.7575 (m-40) cc_final: 0.7235 (t0)
REVERT: A  248 LYS cc_start: 0.8036 (tppt) cc_final: 0.7717 (mtpp)
REVERT: A  297 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7681 (mm-30)
REVERT: A  305 CYS cc_start: 0.8041 (m) cc_final: 0.7500 (m)
REVERT: A  318 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6107 (tp30)
REVERT: A  349 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7759 (mtpm)
REVERT: B    4 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4365 (tt)
REVERT: B   15 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6864 (tppp)
REVERT: B   16 ASN cc_start: 0.8711 (m-40) cc_final: 0.8343 (m110)
REVERT: B   19 ARG cc_start: 0.7105 (mtm110) cc_final: 0.6835 (ttp80)
REVERT: B  189 SER cc_start: 0.7369 (OUTLIER) cc_final: 0.7075 (t)
REVERT: S   34 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5429 (tpt)
REVERT: S  206 ARG cc_start: 0.6934 (tpp-160) cc_final: 0.6671 (tpp80)
  outliers start: 38
  outliers final: 19
  residues processed: 181
  average time/residue: 1.0173
  time to fit residues: 198.0139
Evaluate side-chains
  172 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 THR
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain R residue  277 ILE
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0020
   chunk 80 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    1.1192

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

Flipped N/Q/H residues before XYZ refinement:
** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 155 HIS
S 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.195392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154269 restraints weight = 10783.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 2.97
r_work: 0.4040 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8771  Z= 0.198
  Angle     :  0.684  11.177  11888  Z= 0.339
  Chirality :  0.045   0.357   1354
  Planarity :  0.003   0.038   1489
  Dihedral  :  5.837  76.408   1245
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 24.15 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1081
  helix:  1.33 (0.28), residues: 366
  sheet: -0.74 (0.31), residues: 268
  loop : -1.05 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  82 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.010   0.001   PHE S 200 
 TYR   0.014   0.001   TYR S 223 
 ARG   0.005   0.000   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: R  199 CYS cc_start: 0.6990 (p) cc_final: 0.6537 (m)
REVERT: R  243 TRP cc_start: 0.6583 (t-100) cc_final: 0.6096 (t-100)
REVERT: R  259 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.6238 (t70)
REVERT: A   25 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6534 (tp30)
REVERT: A   33 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.5998 (mp0)
REVERT: A   53 MET cc_start: 0.7850 (mpt) cc_final: 0.7424 (mpt)
REVERT: A  248 LYS cc_start: 0.8032 (tppt) cc_final: 0.7734 (mtpp)
REVERT: A  297 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: A  305 CYS cc_start: 0.8047 (m) cc_final: 0.7504 (m)
REVERT: A  318 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5994 (tp30)
REVERT: B    4 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4278 (tt)
REVERT: B   15 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6809 (tppp)
REVERT: B   16 ASN cc_start: 0.8759 (m-40) cc_final: 0.8481 (m110)
REVERT: B   19 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6771 (ttp80)
REVERT: B  189 SER cc_start: 0.7287 (OUTLIER) cc_final: 0.7017 (t)
REVERT: B  262 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6656 (mmm)
REVERT: S   34 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5379 (tpt)
REVERT: S  206 ARG cc_start: 0.6895 (tpp-160) cc_final: 0.6658 (tpp80)
  outliers start: 42
  outliers final: 21
  residues processed: 183
  average time/residue: 1.0168
  time to fit residues: 200.4840
Evaluate side-chains
  179 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 THR
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  259 HIS
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0670
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.194436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.152990 restraints weight = 10772.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 2.97
r_work: 0.4011 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8771  Z= 0.229
  Angle     :  0.713  11.451  11888  Z= 0.355
  Chirality :  0.047   0.379   1354
  Planarity :  0.003   0.038   1489
  Dihedral  :  5.875  76.634   1245
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.32 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.26), residues: 1081
  helix:  1.35 (0.28), residues: 366
  sheet: -0.73 (0.31), residues: 267
  loop : -1.08 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP S  47 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.012   0.001   PHE S 200 
 TYR   0.025   0.002   TYR A 230 
 ARG   0.005   0.000   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  109 MET cc_start: 0.5353 (tpt) cc_final: 0.5134 (mmt)
REVERT: R  199 CYS cc_start: 0.6975 (p) cc_final: 0.6522 (m)
REVERT: R  243 TRP cc_start: 0.6519 (t-100) cc_final: 0.6258 (t-100)
REVERT: R  259 HIS cc_start: 0.6613 (OUTLIER) cc_final: 0.6244 (t70)
REVERT: A   25 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6493 (tp30)
REVERT: A   33 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6145 (mp0)
REVERT: A   53 MET cc_start: 0.7863 (mpt) cc_final: 0.7440 (mpt)
REVERT: A  248 LYS cc_start: 0.8062 (tppt) cc_final: 0.7770 (mtpp)
REVERT: A  297 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7741 (mm-30)
REVERT: A  305 CYS cc_start: 0.8031 (m) cc_final: 0.7497 (m)
REVERT: A  318 GLU cc_start: 0.6285 (mm-30) cc_final: 0.6076 (tp30)
REVERT: A  349 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7748 (mtpm)
REVERT: B   15 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6897 (tppp)
REVERT: B   16 ASN cc_start: 0.8764 (m-40) cc_final: 0.8421 (m110)
REVERT: B   19 ARG cc_start: 0.7053 (mtm110) cc_final: 0.6828 (ttp80)
REVERT: B  135 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8288 (p)
REVERT: B  189 SER cc_start: 0.7336 (OUTLIER) cc_final: 0.7034 (t)
REVERT: B  262 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6647 (mmm)
REVERT: S   34 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5410 (tpt)
REVERT: S  206 ARG cc_start: 0.6829 (tpp-160) cc_final: 0.6609 (tpp80)
  outliers start: 33
  outliers final: 20
  residues processed: 173
  average time/residue: 1.0182
  time to fit residues: 189.3276
Evaluate side-chains
  178 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 THR
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  259 HIS
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 98 optimal weight:   30.0000
   chunk 63 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0020
   chunk 62 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.1996

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

Flipped N/Q/H residues before XYZ refinement:
** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 195 HIS
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.192233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.150838 restraints weight = 10824.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 2.96
r_work: 0.3998 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7053
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8771  Z= 0.270
  Angle     :  0.731  11.691  11888  Z= 0.365
  Chirality :  0.048   0.399   1354
  Planarity :  0.004   0.041   1489
  Dihedral  :  5.957  76.766   1245
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.64 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.26), residues: 1081
  helix:  1.34 (0.27), residues: 365
  sheet: -0.77 (0.31), residues: 267
  loop : -1.10 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 211 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.018   0.002   TYR S 223 
 ARG   0.004   0.000   ARG B 256 

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 149
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  109 MET cc_start: 0.5405 (tpt) cc_final: 0.5199 (mmt)
REVERT: R  199 CYS cc_start: 0.6997 (p) cc_final: 0.6535 (m)
REVERT: R  259 HIS cc_start: 0.6629 (OUTLIER) cc_final: 0.6254 (t70)
REVERT: A   25 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6552 (tp30)
REVERT: A   33 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6173 (mp0)
REVERT: A   53 MET cc_start: 0.7887 (mpt) cc_final: 0.7455 (mpt)
REVERT: A  297 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7792 (mm-30)
REVERT: A  305 CYS cc_start: 0.8068 (m) cc_final: 0.7527 (m)
REVERT: A  318 GLU cc_start: 0.6299 (mm-30) cc_final: 0.6078 (tp30)
REVERT: A  349 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (mtpm)
REVERT: B   15 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6781 (tppp)
REVERT: B   16 ASN cc_start: 0.8768 (m-40) cc_final: 0.8481 (m110)
REVERT: B   19 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6769 (ttp80)
REVERT: B  135 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8349 (p)
REVERT: B  189 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7153 (t)
REVERT: B  262 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6626 (mmm)
REVERT: S   34 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5401 (tpt)
REVERT: S  206 ARG cc_start: 0.6841 (tpp-160) cc_final: 0.6630 (tpp80)
  outliers start: 34
  outliers final: 20
  residues processed: 169
  average time/residue: 1.1132
  time to fit residues: 201.0966
Evaluate side-chains
  170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  124 SER
Chi-restraints excluded: chain R residue  129 LEU
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  219 THR
Chi-restraints excluded: chain R residue  222 TYR
Chi-restraints excluded: chain R residue  241 ILE
Chi-restraints excluded: chain R residue  259 HIS
Chi-restraints excluded: chain R residue  267 LEU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   47 SER
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  331 ASN
Chi-restraints excluded: chain A residue  349 LYS
Chi-restraints excluded: chain B residue   15 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   34 MET
Chi-restraints excluded: chain S residue  159 ASN
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 29 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 104 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 14 optimal weight:   40.0000
   chunk 8 optimal weight:    0.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS
A 195 HIS
** B  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S 159 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.196573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.155752 restraints weight = 10756.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 2.96
r_work: 0.4054 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8771  Z= 0.191
  Angle     :  0.703  11.348  11888  Z= 0.350
  Chirality :  0.046   0.378   1354
  Planarity :  0.003   0.039   1489
  Dihedral  :  5.864  76.616   1245
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 26.39 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.26), residues: 1081
  helix:  1.47 (0.28), residues: 365
  sheet: -0.58 (0.32), residues: 260
  loop : -0.98 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 211 
 HIS   0.008   0.001   HIS A 213 
 PHE   0.011   0.001   PHE S 200 
 TYR   0.023   0.001   TYR A 230 
 ARG   0.005   0.000   ARG B 256 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7603.99 seconds
wall clock time: 130 minutes 14.60 seconds (7814.60 seconds total)