Starting phenix.real_space_refine
on Thu Mar 13 03:25:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8id3_35356/03_2025/8id3_35356.cif"
  }
  resolution = 3.1
  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=   0.012
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      58      5.16       5
     C    5585      2.51       5
     N    1492      2.21       5
     O    1607      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8742
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2566
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 35
    Chain: "S"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1752
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "Y"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 432
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 1762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1762
          Classifications: {'peptide': 225}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 37
    Chain: "R"
      Number of atoms: 2209
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 291, 2198
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 70
      Conformer: "B"
        Number of residues, atoms: 291, 2198
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 70
          bond proxies already assigned to first conformer: 2234
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'7NR': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG R 261 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG R 261 " occ=0.50
  Time building chain proxies: 6.19, per 1000 atoms: 0.71
  Number of scatterers: 8742
  At special positions: 0
  Unit cell: (107.484, 126.75, 117.624, 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      58     16.00
     O    1607      8.00
     N    1492      7.00
     C    5585      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 160 " - pdb=" SG  CYS S 230 " 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: 2.80
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2142

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 12 sheets defined
      35.8% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 25
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.640A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 221 through 225
      removed outlier: 4.051A  pdb=" N   VAL S 225 " --> pdb=" O   ALA S 222 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 7 through 23
    Processing helix  chain 'Y' and resid 29 through 44
      removed outlier: 3.634A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 30
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.805A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.714A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.911A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.057A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'R' and resid 37 through 68
    Processing helix  chain 'R' and resid 76 through 99
      removed outlier: 3.530A  pdb=" N   ASN R  80 " --> pdb=" O   CYS R  76 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU R  81 " --> pdb=" O   LEU R  77 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 109 through 142
      removed outlier: 4.236A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 170
      removed outlier: 3.783A  pdb=" N   ALA R 160 " --> pdb=" O   ALA R 156 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU R 161 " --> pdb=" O   VAL R 157 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA R 167 " --> pdb=" O   TRP R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.763A  pdb=" N   VAL R 175 " --> pdb=" O   LEU R 171 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE R 176 " --> pdb=" O   PRO R 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 171 through 176'
    Processing helix  chain 'R' and resid 200 through 217
      removed outlier: 3.549A  pdb=" N   GLU R 204 " --> pdb=" O   THR R 200 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ILE R 205 " --> pdb=" O   ILE R 201 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER R 206 " --> pdb=" O   PRO R 202 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASP R 208 " --> pdb=" O   GLU R 204 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 244
      removed outlier: 3.545A  pdb=" N   ARG R 240 " --> pdb=" O   ALA R 236 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU R 241 " --> pdb=" O   SER R 237 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 264
      removed outlier: 3.588A  pdb=" N   VAL R 255 " --> pdb=" O   HIS R 251 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER R 256 " --> pdb=" O   GLN R 252 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLN R 257 " --> pdb=" O   ILE R 253 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   PHE R 260 " --> pdb=" O   SER R 256 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N  AARG R 261 " --> pdb=" O   GLN R 257 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 267 through 294
      removed outlier: 3.662A  pdb=" N   PHE R 273 " --> pdb=" O   LEU R 269 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   PHE R 274 " --> pdb=" O   MET R 270 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER R 278 " --> pdb=" O   PHE R 274 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
      removed outlier: 3.945A  pdb=" N   ASN R 291 " --> pdb=" O   ILE R 287 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   PHE R 292 " --> pdb=" O   LEU R 288 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN R 294 " --> pdb=" O   GLN R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 301 through 321
      removed outlier: 3.567A  pdb=" N   ALA R 312 " --> pdb=" O   ALA R 308 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.548A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.564A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.864A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.087A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.515A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 231
      removed outlier: 6.557A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.590A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.758A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   ALA S  40 " --> pdb=" O   LEU S  45 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   LEU S  45 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 141 through 143
      removed outlier: 3.694A  pdb=" N   ALA S 212 " --> pdb=" O   SER S 209 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 147 through 148
      removed outlier: 6.633A  pdb=" N   LEU S 175 " --> pdb=" O   TYR S 191 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   TYR S 191 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   TRP S 177 " --> pdb=" O   LEU S 189 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.561A  pdb=" N   ASP A 200 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 9.196A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.315A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1111 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: 2.46

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2808
        1.34 -     1.46: 1586
        1.46 -     1.57: 4438
        1.57 -     1.69: 1
        1.69 -     1.81: 84
  Bond restraints: 8917
  Sorted by residual:
  bond pdb=" C   LEU A 353 "
       pdb=" N   PHE A 354 "
    ideal  model  delta    sigma   weight residual
    1.329  1.296  0.033 1.40e-02 5.10e+03 5.65e+00
  bond pdb=" N   ARG R  71 "
       pdb=" CA  ARG R  71 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.028 1.17e-02 7.31e+03 5.54e+00
  bond pdb=" N   ARG R  70 "
       pdb=" CA  ARG R  70 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.44e+00
  bond pdb=" N   ARG R  69 "
       pdb=" CA  ARG R  69 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.29e-02 6.01e+03 5.10e+00
  bond pdb=" N   ARG R  68 "
       pdb=" CA  ARG R  68 "
    ideal  model  delta    sigma   weight residual
    1.464  1.489 -0.025 1.30e-02 5.92e+03 3.78e+00
  ... (remaining 8912 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.40: 12068
        5.40 -    10.80: 31
       10.80 -    16.20: 1
       16.20 -    21.59: 0
       21.59 -    26.99: 2
  Bond angle restraints: 12102
  Sorted by residual:
  angle pdb=" CD  ARG R 254 "
        pdb=" NE  ARG R 254 "
        pdb=" CZ  ARG R 254 "
      ideal   model   delta    sigma   weight residual
     124.40   97.41   26.99 1.40e+00 5.10e-01 3.72e+02
  angle pdb=" CA  ASP R 259 "
        pdb=" CB  ASP R 259 "
        pdb=" CG  ASP R 259 "
      ideal   model   delta    sigma   weight residual
     112.60  103.66    8.94 1.00e+00 1.00e+00 7.99e+01
  angle pdb=" CA  GLN R 258 "
        pdb=" CB  GLN R 258 "
        pdb=" CG  GLN R 258 "
      ideal   model   delta    sigma   weight residual
     114.10  130.28  -16.18 2.00e+00 2.50e-01 6.55e+01
  angle pdb=" CA  LEU R  86 "
        pdb=" CB  LEU R  86 "
        pdb=" CG  LEU R  86 "
      ideal   model   delta    sigma   weight residual
     116.30  141.78  -25.48 3.50e+00 8.16e-02 5.30e+01
  angle pdb=" N   VAL R 109 "
        pdb=" CA  VAL R 109 "
        pdb=" C   VAL R 109 "
      ideal   model   delta    sigma   weight residual
     113.71  107.13    6.58 9.50e-01 1.11e+00 4.80e+01
  ... (remaining 12097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 4811
       17.63 -    35.25: 374
       35.25 -    52.88: 63
       52.88 -    70.50: 18
       70.50 -    88.13: 7
  Dihedral angle restraints: 5273
    sinusoidal: 1963
      harmonic: 3310
  Sorted by residual:
  dihedral pdb=" CD  ARG R  69 "
           pdb=" NE  ARG R  69 "
           pdb=" CZ  ARG R  69 "
           pdb=" NH1 ARG R  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.86  -75.86     1      1.00e+01 1.00e-02 7.25e+01
  dihedral pdb=" CB  CYS S 160 "
           pdb=" SG  CYS S 160 "
           pdb=" SG  CYS S 230 "
           pdb=" CB  CYS S 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.16  -65.16     1      1.00e+01 1.00e-02 5.57e+01
  dihedral pdb=" CA  HIS R 142 "
           pdb=" C   HIS R 142 "
           pdb=" N   LEU R 143 "
           pdb=" CA  LEU R 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.85  -19.15     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5270 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1223
       0.066 -    0.132: 178
       0.132 -    0.197: 11
       0.197 -    0.263: 0
       0.263 -    0.329: 2
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CB  ILE R  89 "
            pdb=" CA  ILE R  89 "
            pdb=" CG1 ILE R  89 "
            pdb=" CG2 ILE R  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.97   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C04 7NR R 401 "
            pdb=" C05 7NR R 401 "
            pdb=" C06 7NR R 401 "
            pdb=" O01 7NR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.76    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  ARG R  71 "
            pdb=" N   ARG R  71 "
            pdb=" C   ARG R  71 "
            pdb=" CB  ARG R  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.53e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1520
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  69 "    1.062 9.50e-02 1.11e+02   4.76e-01 1.37e+02
        pdb=" NE  ARG R  69 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  69 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  69 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  69 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 115 "    0.082 2.00e-02 2.50e+03   5.02e-02 4.41e+01
        pdb=" CG  PHE R 115 "   -0.074 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 115 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 115 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 115 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 115 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 115 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R  68 "   -0.569 9.50e-02 1.11e+02   2.55e-01 3.98e+01
        pdb=" NE  ARG R  68 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG R  68 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG R  68 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG R  68 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1517 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 764
        2.74 -     3.28: 8404
        3.28 -     3.82: 13890
        3.82 -     4.36: 16479
        4.36 -     4.90: 29602
  Nonbonded interactions: 69139
  Sorted by model distance:
  nonbonded pdb=" CD  ARG R 254 "
            pdb=" NH1 ARG R 254 "
     model   vdw
     2.199 2.816
  nonbonded pdb=" O   ASN A 347 "
            pdb=" OD1 ASP A 350 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD2 ASP B 228 "
            pdb=" NZ  LYS A 209 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP Y  48 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OE1 GLN A  52 "
            pdb=" ND2 ASN A 331 "
     model   vdw
     2.300 3.120
  ... (remaining 69134 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.530
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
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      :  0.005   0.094   8917  Z= 0.297
  Angle     :  0.854  26.993  12102  Z= 0.505
  Chirality :  0.048   0.329   1414
  Planarity :  0.015   0.476   1520
  Dihedral  : 13.646  88.129   3128
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  0.33 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.24), residues: 1126
  helix: -0.23 (0.27), residues: 372
  sheet: -0.72 (0.30), residues: 289
  loop : -1.57 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 104 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.082   0.003   PHE R 115 
 TYR   0.013   0.001   TYR R 165 
 ARG   0.008   0.000   ARG S 161 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 157
  time to evaluate  : 1.058 
Fit side-chains
REVERT: B  290 ASP cc_start: 0.7274 (m-30) cc_final: 0.6962 (m-30)
REVERT: A  229 ASP cc_start: 0.8172 (t70) cc_final: 0.7757 (t70)
REVERT: A  245 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7288 (tm-30)
REVERT: A  298 GLU cc_start: 0.7887 (pt0) cc_final: 0.7473 (pt0)
REVERT: A  354 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.7052 (t80)
  outliers start: 6
  outliers final: 1
  residues processed: 161
  average time/residue: 0.2248
  time to fit residues: 48.7261
Evaluate side-chains
  141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue  106 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 46 optimal weight:   50.0000
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    1.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.159579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.109857 restraints weight = 34038.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 4.44
r_work: 0.3002 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8917  Z= 0.241
  Angle     :  0.583   7.303  12102  Z= 0.309
  Chirality :  0.043   0.155   1414
  Planarity :  0.004   0.051   1520
  Dihedral  :  5.550  56.879   1250
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  7.16 %
    Favored  : 91.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.70 (0.25), residues: 1126
  helix:  0.67 (0.28), residues: 365
  sheet: -0.50 (0.30), residues: 297
  loop : -1.29 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 207 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.018   0.002   PHE R 177 
 TYR   0.016   0.001   TYR R 165 
 ARG   0.004   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 0.988 
Fit side-chains
REVERT: S  203 ARG cc_start: 0.5999 (mtm110) cc_final: 0.5736 (mtm-85)
REVERT: A  229 ASP cc_start: 0.8059 (t70) cc_final: 0.7550 (t70)
REVERT: A  330 LYS cc_start: 0.7957 (mptt) cc_final: 0.7690 (mmtm)
REVERT: A  354 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6793 (t80)
REVERT: R  178 ARG cc_start: 0.7304 (mmt90) cc_final: 0.6874 (mmm160)
  outliers start: 7
  outliers final: 2
  residues processed: 147
  average time/residue: 0.2269
  time to fit residues: 45.2049
Evaluate side-chains
  139 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
A  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.161250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.114033 restraints weight = 22635.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.46
r_work: 0.3127 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3081
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3081 r_free = 0.3081    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3081
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8917  Z= 0.165
  Angle     :  0.534   8.540  12102  Z= 0.280
  Chirality :  0.042   0.144   1414
  Planarity :  0.004   0.047   1520
  Dihedral  :  4.914  57.023   1248
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.76 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.46 (0.25), residues: 1126
  helix:  0.93 (0.28), residues: 377
  sheet: -0.33 (0.30), residues: 298
  loop : -1.28 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.020   0.001   TYR R 165 
 ARG   0.003   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7584 (ppt170) cc_final: 0.7088 (pmt-80)
REVERT: A  229 ASP cc_start: 0.7984 (t70) cc_final: 0.7489 (t70)
REVERT: A  276 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7731 (mp0)
REVERT: A  330 LYS cc_start: 0.7955 (mptt) cc_final: 0.7696 (mmtm)
  outliers start: 13
  outliers final: 10
  residues processed: 141
  average time/residue: 0.2016
  time to fit residues: 39.8107
Evaluate side-chains
  135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue   46 GLU
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 83 optimal weight:    0.1980
   chunk 105 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 89 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
A 195 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.162647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.117573 restraints weight = 15915.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.80
r_work: 0.3158 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.1678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8917  Z= 0.153
  Angle     :  0.511   7.416  12102  Z= 0.269
  Chirality :  0.041   0.142   1414
  Planarity :  0.003   0.046   1520
  Dihedral  :  4.693  57.014   1248
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 10.09 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.25), residues: 1126
  helix:  1.17 (0.29), residues: 378
  sheet: -0.35 (0.29), residues: 298
  loop : -1.17 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE S  68 
 TYR   0.011   0.001   TYR R 165 
 ARG   0.004   0.000   ARG B 314 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.866 
Fit side-chains
REVERT: B  259 GLN cc_start: 0.7639 (tt0) cc_final: 0.6723 (mt0)
REVERT: A  229 ASP cc_start: 0.8028 (t70) cc_final: 0.7500 (t70)
REVERT: A  240 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7364 (pmm)
REVERT: A  276 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7640 (mp0)
REVERT: A  330 LYS cc_start: 0.7966 (mptt) cc_final: 0.7717 (mmtm)
  outliers start: 17
  outliers final: 12
  residues processed: 135
  average time/residue: 0.2079
  time to fit residues: 38.8396
Evaluate side-chains
  135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  142 THR
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.155866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.106223 restraints weight = 16382.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 2.96
r_work: 0.3103 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8917  Z= 0.283
  Angle     :  0.566   7.506  12102  Z= 0.299
  Chirality :  0.043   0.147   1414
  Planarity :  0.004   0.050   1520
  Dihedral  :  4.864  58.048   1248
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.71 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.25), residues: 1126
  helix:  1.13 (0.29), residues: 380
  sheet: -0.29 (0.29), residues: 304
  loop : -1.29 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  36 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.018   0.002   PHE S  68 
 TYR   0.014   0.002   TYR B  59 
 ARG   0.005   0.000   ARG B 314 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8025 (t70) cc_final: 0.7475 (t70)
REVERT: A  240 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7434 (pmm)
REVERT: A  276 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7649 (mp0)
REVERT: A  330 LYS cc_start: 0.7993 (mptt) cc_final: 0.7734 (mmtm)
REVERT: R  214 LEU cc_start: 0.8644 (tp) cc_final: 0.8358 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 139
  average time/residue: 0.2159
  time to fit residues: 40.9862
Evaluate side-chains
  143 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 92 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.159640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.111967 restraints weight = 22749.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 3.48
r_work: 0.3089 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8917  Z= 0.224
  Angle     :  0.542   7.456  12102  Z= 0.286
  Chirality :  0.042   0.140   1414
  Planarity :  0.004   0.049   1520
  Dihedral  :  4.859  57.529   1248
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.36 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.25 (0.25), residues: 1126
  helix:  1.19 (0.29), residues: 380
  sheet: -0.23 (0.30), residues: 304
  loop : -1.27 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.013   0.001   PHE S  68 
 TYR   0.011   0.001   TYR B  59 
 ARG   0.007   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: S  231 MET cc_start: 0.8759 (ttp) cc_final: 0.8551 (ttt)
REVERT: A  229 ASP cc_start: 0.8014 (t70) cc_final: 0.7441 (t70)
REVERT: A  276 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7613 (mp0)
REVERT: A  330 LYS cc_start: 0.7998 (mptt) cc_final: 0.7740 (mmtm)
REVERT: R  104 TRP cc_start: 0.8461 (t-100) cc_final: 0.8112 (t60)
  outliers start: 18
  outliers final: 16
  residues processed: 134
  average time/residue: 0.2208
  time to fit residues: 40.8511
Evaluate side-chains
  142 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  242 THR
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 106 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.160337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.113173 restraints weight = 27640.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 4.00
r_work: 0.3063 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8917  Z= 0.194
  Angle     :  0.533  10.073  12102  Z= 0.278
  Chirality :  0.042   0.138   1414
  Planarity :  0.004   0.050   1520
  Dihedral  :  4.667  57.059   1248
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.12 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.13 (0.26), residues: 1126
  helix:  1.30 (0.29), residues: 380
  sheet: -0.18 (0.30), residues: 295
  loop : -1.18 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 207 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.020   0.001   PHE S  68 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.007   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  229 ASP cc_start: 0.8048 (t70) cc_final: 0.7497 (t70)
REVERT: A  240 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7046 (pmm)
REVERT: A  276 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7783 (mp0)
REVERT: R  104 TRP cc_start: 0.8497 (t-100) cc_final: 0.8206 (t60)
  outliers start: 19
  outliers final: 16
  residues processed: 132
  average time/residue: 0.2217
  time to fit residues: 39.7955
Evaluate side-chains
  141 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  242 THR
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 0 optimal weight:   40.0000
   chunk 28 optimal weight:    0.0060
   chunk 71 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0870
   chunk 51 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6176

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
A 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.161375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.112377 restraints weight = 17719.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 3.09
r_work: 0.3177 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8917  Z= 0.141
  Angle     :  0.502   8.941  12102  Z= 0.259
  Chirality :  0.041   0.140   1414
  Planarity :  0.003   0.049   1520
  Dihedral  :  4.416  56.234   1248
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.67 %
    Favored  : 84.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.04 (0.26), residues: 1126
  helix:  1.49 (0.29), residues: 379
  sheet: -0.10 (0.30), residues: 292
  loop : -1.11 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE S  68 
 TYR   0.008   0.001   TYR R 165 
 ARG   0.006   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.013 
Fit side-chains
REVERT: S   93 MET cc_start: 0.7814 (ttt) cc_final: 0.7581 (ttt)
REVERT: S  231 MET cc_start: 0.8746 (ttp) cc_final: 0.8540 (ttt)
REVERT: A  229 ASP cc_start: 0.8010 (t70) cc_final: 0.7438 (t70)
REVERT: A  240 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6963 (pmm)
REVERT: A  276 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7818 (mp0)
REVERT: R  104 TRP cc_start: 0.8437 (t-100) cc_final: 0.8232 (t60)
  outliers start: 16
  outliers final: 14
  residues processed: 135
  average time/residue: 0.2287
  time to fit residues: 42.2871
Evaluate side-chains
  139 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 100 optimal weight:    0.0980
   chunk 79 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0980
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.161006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112051 restraints weight = 19968.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 3.42
r_work: 0.3142 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3107
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3107 r_free = 0.3107    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3107
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8917  Z= 0.145
  Angle     :  0.522  13.960  12102  Z= 0.264
  Chirality :  0.041   0.154   1414
  Planarity :  0.003   0.050   1520
  Dihedral  :  4.318  56.052   1248
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.53 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.14 (0.26), residues: 1126
  helix:  1.50 (0.29), residues: 382
  sheet: -0.07 (0.30), residues: 294
  loop : -0.98 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE S  68 
 TYR   0.009   0.001   TYR R 165 
 ARG   0.006   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.020 
Fit side-chains
REVERT: S   46 GLU cc_start: 0.8541 (pt0) cc_final: 0.8330 (pt0)
REVERT: S  231 MET cc_start: 0.8767 (ttp) cc_final: 0.8557 (ttt)
REVERT: A  229 ASP cc_start: 0.7975 (t70) cc_final: 0.7386 (t70)
REVERT: A  240 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6915 (pmm)
REVERT: A  276 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7828 (mp0)
REVERT: A  330 LYS cc_start: 0.7907 (mptt) cc_final: 0.7662 (mmtm)
REVERT: R  104 TRP cc_start: 0.8514 (t-100) cc_final: 0.8274 (t60)
  outliers start: 17
  outliers final: 14
  residues processed: 139
  average time/residue: 0.2123
  time to fit residues: 40.7181
Evaluate side-chains
  144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 102 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0370
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.163457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117529 restraints weight = 28513.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 4.10
r_work: 0.3121 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8917  Z= 0.145
  Angle     :  0.516  13.092  12102  Z= 0.262
  Chirality :  0.041   0.138   1414
  Planarity :  0.003   0.050   1520
  Dihedral  :  4.274  55.625   1248
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.64 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.22 (0.26), residues: 1126
  helix:  1.55 (0.28), residues: 382
  sheet:  0.04 (0.30), residues: 293
  loop : -0.97 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 207 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE S  68 
 TYR   0.009   0.001   TYR R 165 
 ARG   0.006   0.000   ARG R 178 

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.059 
Fit side-chains
REVERT: S   93 MET cc_start: 0.7909 (ttt) cc_final: 0.7694 (ttt)
REVERT: A  229 ASP cc_start: 0.7988 (t70) cc_final: 0.7398 (t70)
REVERT: A  240 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7001 (pmm)
REVERT: A  276 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7883 (mp0)
REVERT: A  330 LYS cc_start: 0.7956 (mptt) cc_final: 0.7713 (mmtm)
REVERT: A  333 GLN cc_start: 0.8177 (tp40) cc_final: 0.7744 (mm-40)
REVERT: R  104 TRP cc_start: 0.8499 (t-100) cc_final: 0.8285 (t60)
  outliers start: 17
  outliers final: 15
  residues processed: 137
  average time/residue: 0.2186
  time to fit residues: 41.5476
Evaluate side-chains
  144 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   91 THR
Chi-restraints excluded: chain S residue  139 ILE
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  168 VAL
Chi-restraints excluded: chain R residue  197 ILE
Chi-restraints excluded: chain R residue  285 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0770
   chunk 102 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 100 optimal weight:    0.3980
   chunk 23 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.164110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117806 restraints weight = 21482.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.51
r_work: 0.3169 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8917  Z= 0.138
  Angle     :  0.509  12.320  12102  Z= 0.259
  Chirality :  0.041   0.138   1414
  Planarity :  0.003   0.050   1520
  Dihedral  :  4.224  55.230   1248
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.86 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.31 (0.26), residues: 1126
  helix:  1.64 (0.28), residues: 382
  sheet:  0.09 (0.30), residues: 293
  loop : -0.92 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  63 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.018   0.001   PHE S  68 
 TYR   0.008   0.001   TYR R 165 
 ARG   0.006   0.000   ARG R 178 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5714.20 seconds
wall clock time: 98 minutes 21.64 seconds (5901.64 seconds total)