Starting phenix.real_space_refine
on Thu Mar 13 10:28:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lll_23425/03_2025/7lll_23425.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    5670      2.51       5
     N    1555      2.21       5
     O    1659      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 8940
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1928
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2615
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "P"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 231
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "R"
      Number of atoms: 2749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2749
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 73}
          Link IDs: {'PTRANS': 13, 'TRANS': 352}
          Chain breaks: 4
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 313
          Unresolved non-hydrogen angles: 414
          Unresolved non-hydrogen dihedrals: 281
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 210
  Time building chain proxies: 5.25, per 1000 atoms: 0.59
  Number of scatterers: 8940
  At special positions: 0
  Unit cell: (87.87, 103.53, 174, 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      56     16.00
     O    1659      8.00
     N    1555      7.00
     C    5670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  71 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  62 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  85 " - pdb=" SG  CYS R 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 226 " - pdb=" SG  CYS R 296 " distance=2.05

  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: 2.10
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 13 sheets defined
      38.1% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 3.772A  pdb=" N   ARG A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 33
      removed outlier: 3.601A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 278
      removed outlier: 3.785A  pdb=" N   LYS A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   LEU A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.659A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.785A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.655A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP A 343 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 375
      removed outlier: 3.705A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
    Processing helix  chain 'A' and resid 380 through 391
      removed outlier: 3.833A  pdb=" N   MET A 386 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 23
      removed outlier: 4.258A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ASP B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B  21 " --> pdb=" O   GLN B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.699A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 21
      removed outlier: 3.854A  pdb=" N   GLN G  11 " --> pdb=" O   ALA G   7 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL G  16 " --> pdb=" O   ALA G  12 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLU G  17 " --> pdb=" O   ARG G  13 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 33
    Processing helix  chain 'G' and resid 34 through 44
      removed outlier: 4.228A  pdb=" N   GLU G  42 " --> pdb=" O   MET G  38 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.815A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 4.182A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 28
      removed outlier: 4.144A  pdb=" N   SER P   8 " --> pdb=" O   GLY P   4 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   MET P  14 " --> pdb=" O   LEU P  10 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ALA P  18 " --> pdb=" O   MET P  14 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL P  19 " --> pdb=" O   GLU P  15 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG P  20 " --> pdb=" O   GLU P  16 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TRP P  25 " --> pdb=" O   LEU P  21 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU P  26 " --> pdb=" O   PHE P  22 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS P  27 " --> pdb=" O   ILE P  23 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ASN P  28 " --> pdb=" O   GLU P  24 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 3.720A  pdb=" N   VAL R  36 " --> pdb=" O   LEU R  32 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLN R  37 " --> pdb=" O   TRP R  33 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   CYS R  46 " --> pdb=" O   TYR R  42 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ARG R  48 " --> pdb=" O   ARG R  44 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   SER R  49 " --> pdb=" O   GLN R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 93
    Processing helix  chain 'R' and resid 139 through 149
      removed outlier: 4.164A  pdb=" N   TYR R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ILE R 146 " --> pdb=" O   LEU R 142 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ILE R 147 " --> pdb=" O   PHE R 143 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 169
      removed outlier: 3.801A  pdb=" N   LEU R 154 " --> pdb=" O   VAL R 150 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE R 156 " --> pdb=" O   TYR R 152 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER R 157 " --> pdb=" O   ALA R 153 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   LEU R 159 " --> pdb=" O   SER R 155 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL R 160 " --> pdb=" O   PHE R 156 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER R 163 " --> pdb=" O   LEU R 159 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU R 166 " --> pdb=" O   ALA R 162 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU R 167 " --> pdb=" O   SER R 163 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   PHE R 169 " --> pdb=" O   ILE R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 204
      removed outlier: 3.822A  pdb=" N   HIS R 180 " --> pdb=" O   ARG R 176 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASN R 182 " --> pdb=" O   TYR R 178 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU R 189 " --> pdb=" O   ALA R 185 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU R 192 " --> pdb=" O   ILE R 188 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE R 196 " --> pdb=" O   LEU R 192 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LYS R 197 " --> pdb=" O   SER R 193 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP R 198 " --> pdb=" O   VAL R 194 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA R 199 " --> pdb=" O   PHE R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 223 through 228
      removed outlier: 4.235A  pdb=" N   ARG R 227 " --> pdb=" O   SER R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 228 through 237
      removed outlier: 3.983A  pdb=" N   GLN R 234 " --> pdb=" O   PHE R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 244 through 251
    Processing helix  chain 'R' and resid 264 through 268
    Processing helix  chain 'R' and resid 269 through 274
      removed outlier: 3.500A  pdb=" N   TRP R 274 " --> pdb=" O   VAL R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 276 through 280
    Processing helix  chain 'R' and resid 281 through 291
      removed outlier: 3.603A  pdb=" N   VAL R 287 " --> pdb=" O   PRO R 283 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR R 289 " --> pdb=" O   GLY R 285 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR R 291 " --> pdb=" O   VAL R 287 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 298
      removed outlier: 3.817A  pdb=" N   THR R 298 " --> pdb=" O   GLY R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 308
    Processing helix  chain 'R' and resid 310 through 329
      removed outlier: 3.509A  pdb=" N   PHE R 315 " --> pdb=" O   LEU R 311 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU R 322 " --> pdb=" O   GLY R 318 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ILE R 323 " --> pdb=" O   VAL R 319 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   PHE R 324 " --> pdb=" O   ASN R 320 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 338
      removed outlier: 3.765A  pdb=" N   LEU R 335 " --> pdb=" O   VAL R 331 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA R 337 " --> pdb=" O   SER R 333 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 345 through 361
      removed outlier: 3.866A  pdb=" N   THR R 355 " --> pdb=" O   LYS R 351 " (cutoff:3.500A)
      Proline residue:  R 358  - end of helix
    Processing helix  chain 'R' and resid 362 through 367
    Processing helix  chain 'R' and resid 378 through 391
      removed outlier: 3.839A  pdb=" N   THR R 386 " --> pdb=" O   ILE R 382 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   SER R 389 " --> pdb=" O   PHE R 385 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 393 through 404
      removed outlier: 3.538A  pdb=" N   PHE R 404 " --> pdb=" O   ILE R 400 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 419
      removed outlier: 3.693A  pdb=" N   ARG R 414 " --> pdb=" O   GLN R 410 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG R 419 " --> pdb=" O   LYS R 415 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214
      removed outlier: 3.815A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A  44 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 245 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.526A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.640A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.663A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.029A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.638A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.841A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 297
      removed outlier: 6.655A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320
      removed outlier: 4.077A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 329 " --> pdb=" O   LYS B 337 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
    Processing sheet with id=AB2, first strand: chain 'N' and resid 45 through 51
      removed outlier: 6.708A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL N  93 " --> pdb=" O   GLN N  39 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   THR N 122 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 73
      removed outlier: 3.770A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 80 through 81
      removed outlier: 4.039A  pdb=" N   VAL R  81 " --> pdb=" O   ARG R 102 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ARG R 102 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    269 hydrogen bonds defined for protein.
    753 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: 2.18

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2357
        1.33 -     1.45: 1817
        1.45 -     1.58: 4870
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 9120
  Sorted by residual:
  bond pdb=" N   VAL R 370 "
       pdb=" CA  VAL R 370 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 8.60e-03 1.35e+04 1.47e+01
  bond pdb=" C   TRP R  72 "
       pdb=" N   PRO R  73 "
    ideal  model  delta    sigma   weight residual
    1.332  1.377 -0.045 1.26e-02 6.30e+03 1.30e+01
  bond pdb=" C   LEU R 311 "
       pdb=" N   PRO R 312 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.046 1.36e-02 5.41e+03 1.17e+01
  bond pdb=" N   LEU R 359 "
       pdb=" CA  LEU R 359 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.043 1.27e-02 6.20e+03 1.14e+01
  bond pdb=" N   GLU R 294 "
       pdb=" CA  GLU R 294 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.038 1.23e-02 6.61e+03 9.75e+00
  ... (remaining 9115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 11989
        2.37 -     4.73: 339
        4.73 -     7.10: 26
        7.10 -     9.46: 4
        9.46 -    11.83: 1
  Bond angle restraints: 12359
  Sorted by residual:
  angle pdb=" N   VAL R 370 "
        pdb=" CA  VAL R 370 "
        pdb=" C   VAL R 370 "
      ideal   model   delta    sigma   weight residual
     113.71  107.88    5.83 9.50e-01 1.11e+00 3.77e+01
  angle pdb=" N   PRO R 358 "
        pdb=" CA  PRO R 358 "
        pdb=" C   PRO R 358 "
      ideal   model   delta    sigma   weight residual
     113.65  121.59   -7.94 1.35e+00 5.49e-01 3.46e+01
  angle pdb=" C   VAL R 281 "
        pdb=" N   VAL R 282 "
        pdb=" CA  VAL R 282 "
      ideal   model   delta    sigma   weight residual
     120.33  125.01   -4.68 8.00e-01 1.56e+00 3.42e+01
  angle pdb=" C   TRP R  72 "
        pdb=" N   PRO R  73 "
        pdb=" CA  PRO R  73 "
      ideal   model   delta    sigma   weight residual
     119.92  125.12   -5.20 1.07e+00 8.73e-01 2.36e+01
  angle pdb=" N   LEU R 268 "
        pdb=" CA  LEU R 268 "
        pdb=" C   LEU R 268 "
      ideal   model   delta    sigma   weight residual
     112.41  106.10    6.31 1.30e+00 5.92e-01 2.36e+01
  ... (remaining 12354 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4911
       17.84 -    35.68: 425
       35.68 -    53.52: 65
       53.52 -    71.36: 5
       71.36 -    89.20: 8
  Dihedral angle restraints: 5414
    sinusoidal: 2061
      harmonic: 3353
  Sorted by residual:
  dihedral pdb=" CB  CYS R 226 "
           pdb=" SG  CYS R 226 "
           pdb=" SG  CYS R 296 "
           pdb=" CB  CYS R 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.85  -51.85     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CA  PHE R 230 "
           pdb=" C   PHE R 230 "
           pdb=" N   LEU R 231 "
           pdb=" CA  LEU R 231 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.90   28.10     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  TYR R 291 "
           pdb=" C   TYR R 291 "
           pdb=" N   GLU R 292 "
           pdb=" CA  GLU R 292 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.48  -25.52     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 5411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1150
       0.068 -    0.136: 206
       0.136 -    0.203: 27
       0.203 -    0.271: 4
       0.271 -    0.339: 2
  Chirality restraints: 1389
  Sorted by residual:
  chirality pdb=" CA  PRO R 358 "
            pdb=" N   PRO R 358 "
            pdb=" C   PRO R 358 "
            pdb=" CB  PRO R 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CA  MET R 303 "
            pdb=" N   MET R 303 "
            pdb=" C   MET R 303 "
            pdb=" CB  MET R 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CA  PHE R 280 "
            pdb=" N   PHE R 280 "
            pdb=" C   PHE R 280 "
            pdb=" CB  PHE R 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1386 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 383 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" C   LYS R 383 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS R 383 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU R 384 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL G  54 "   -0.064 5.00e-02 4.00e+02   9.69e-02 1.50e+01
        pdb=" N   PRO G  55 "    0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO G  55 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO G  55 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU R 294 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   GLU R 294 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLU R 294 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLY R 295 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 227
        2.68 -     3.23: 8467
        3.23 -     3.79: 11765
        3.79 -     4.34: 16467
        4.34 -     4.90: 27069
  Nonbonded interactions: 63995
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" O   ALA B  56 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR A 369 "
            pdb=" OD1 ASN A 371 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR B 145 "
            pdb=" OD2 ASP B 186 "
     model   vdw
     2.199 3.040
  ... (remaining 63990 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.020
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   9120  Z= 0.382
  Angle     :  0.901  11.826  12359  Z= 0.591
  Chirality :  0.055   0.339   1389
  Planarity :  0.005   0.097   1580
  Dihedral  : 13.684  89.195   3224
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.05 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.22), residues: 1129
  helix: -2.86 (0.23), residues: 382
  sheet: -3.15 (0.34), residues: 188
  loop : -2.55 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.006   0.001   HIS G  44 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.011   0.001   TYR A 360 
 ARG   0.007   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 1.053 
Fit side-chains
REVERT: A   14 ASN cc_start: 0.7611 (m110) cc_final: 0.7407 (m110)
REVERT: R  204 MET cc_start: 0.5246 (ttt) cc_final: 0.4968 (tmm)
REVERT: R  224 LEU cc_start: 0.8116 (tp) cc_final: 0.7749 (mm)
REVERT: R  267 ARG cc_start: 0.8189 (mmt180) cc_final: 0.7670 (ptm160)
REVERT: R  351 LYS cc_start: 0.7412 (tptt) cc_final: 0.6745 (tttm)
REVERT: R  371 MET cc_start: 0.6187 (ppp) cc_final: 0.5239 (ppp)
REVERT: R  414 ARG cc_start: 0.7097 (tpp-160) cc_final: 0.6026 (ttm110)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2361
  time to fit residues: 50.6821
Evaluate side-chains
  127 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:   50.0000
   chunk 47 optimal weight:    0.4980
   chunk 28 optimal weight:    0.3980
   chunk 57 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 268 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.168956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143362 restraints weight = 10514.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141403 restraints weight = 18708.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.138022 restraints weight = 20722.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9120  Z= 0.170
  Angle     :  0.616  10.478  12359  Z= 0.327
  Chirality :  0.042   0.160   1389
  Planarity :  0.005   0.074   1580
  Dihedral  :  5.241  25.087   1247
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.32 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.22), residues: 1129
  helix: -2.16 (0.23), residues: 406
  sheet: -2.67 (0.34), residues: 196
  loop : -2.42 (0.24), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.011   0.001   HIS R 171 
 PHE   0.018   0.001   PHE R 280 
 TYR   0.014   0.001   TYR A 360 
 ARG   0.003   0.000   ARG B 197 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A   31 GLN cc_start: 0.7764 (mm110) cc_final: 0.7460 (tp40)
REVERT: B   59 TYR cc_start: 0.8716 (m-80) cc_final: 0.8415 (m-80)
REVERT: G   32 LYS cc_start: 0.8608 (mmtm) cc_final: 0.7927 (ttmm)
REVERT: R  345 ILE cc_start: 0.6748 (mm) cc_final: 0.6461 (mt)
REVERT: R  351 LYS cc_start: 0.7242 (tptt) cc_final: 0.6841 (tttt)
REVERT: R  371 MET cc_start: 0.5988 (ppp) cc_final: 0.4981 (ppp)
REVERT: R  414 ARG cc_start: 0.6761 (tpp-160) cc_final: 0.6279 (ttm110)
  outliers start: 8
  outliers final: 4
  residues processed: 145
  average time/residue: 0.2593
  time to fit residues: 49.9328
Evaluate side-chains
  124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 120
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  366 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0470
   chunk 106 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 85 optimal weight:   10.0000
   chunk 88 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.6682

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.169765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.152352 restraints weight = 10439.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150016 restraints weight = 22230.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.149349 restraints weight = 25141.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9120  Z= 0.219
  Angle     :  0.620  10.673  12359  Z= 0.325
  Chirality :  0.042   0.171   1389
  Planarity :  0.004   0.059   1580
  Dihedral  :  5.077  23.685   1247
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.77 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.23), residues: 1129
  helix: -1.68 (0.25), residues: 406
  sheet: -2.41 (0.36), residues: 189
  loop : -2.28 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 297 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.020   0.002   PHE N 108 
 TYR   0.017   0.002   TYR R 291 
 ARG   0.003   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.021 
Fit side-chains
REVERT: R  230 PHE cc_start: 0.6910 (m-10) cc_final: 0.6482 (t80)
REVERT: R  345 ILE cc_start: 0.6616 (mm) cc_final: 0.6287 (mt)
REVERT: R  351 LYS cc_start: 0.7454 (tptt) cc_final: 0.6745 (tttt)
REVERT: R  371 MET cc_start: 0.6413 (ppp) cc_final: 0.5313 (ppp)
REVERT: R  414 ARG cc_start: 0.6719 (tpp-160) cc_final: 0.6375 (ttm110)
  outliers start: 11
  outliers final: 9
  residues processed: 131
  average time/residue: 0.2361
  time to fit residues: 42.1430
Evaluate side-chains
  121 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   24 ASN
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  357 ILE
Chi-restraints excluded: chain R residue  366 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:   50.0000
   chunk 68 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 103 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.186349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.161342 restraints weight = 9975.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.159101 restraints weight = 20881.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.159006 restraints weight = 21295.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9120  Z= 0.155
  Angle     :  0.554  11.017  12359  Z= 0.288
  Chirality :  0.040   0.163   1389
  Planarity :  0.004   0.055   1580
  Dihedral  :  4.682  23.928   1247
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.96 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.24), residues: 1129
  helix: -1.38 (0.25), residues: 413
  sheet: -2.10 (0.36), residues: 197
  loop : -2.21 (0.25), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.002   0.001   HIS G  44 
 PHE   0.024   0.001   PHE R 280 
 TYR   0.017   0.001   TYR R 291 
 ARG   0.003   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.899 
Fit side-chains
REVERT: G   32 LYS cc_start: 0.8594 (mmtm) cc_final: 0.7925 (ttmm)
REVERT: R  230 PHE cc_start: 0.7020 (m-10) cc_final: 0.6388 (t80)
REVERT: R  345 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6129 (tp)
REVERT: R  414 ARG cc_start: 0.6558 (tpp-160) cc_final: 0.6107 (ttm110)
  outliers start: 19
  outliers final: 10
  residues processed: 126
  average time/residue: 0.2347
  time to fit residues: 40.0368
Evaluate side-chains
  116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.166693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.142459 restraints weight = 10479.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.140213 restraints weight = 21772.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139151 restraints weight = 22565.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9120  Z= 0.188
  Angle     :  0.568  10.916  12359  Z= 0.297
  Chirality :  0.041   0.164   1389
  Planarity :  0.004   0.053   1580
  Dihedral  :  4.673  22.770   1247
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.36 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.24), residues: 1129
  helix: -1.15 (0.26), residues: 411
  sheet: -2.02 (0.36), residues: 196
  loop : -2.19 (0.25), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 297 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.017   0.001   TYR R 291 
 ARG   0.004   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.902 
Fit side-chains
REVERT: R  230 PHE cc_start: 0.6956 (m-10) cc_final: 0.6442 (t80)
REVERT: R  345 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6099 (tp)
REVERT: R  371 MET cc_start: 0.6435 (ppp) cc_final: 0.5140 (ppp)
  outliers start: 16
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2285
  time to fit residues: 37.6141
Evaluate side-chains
  113 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 79 optimal weight:   50.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
N  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.162255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.138114 restraints weight = 10650.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.135262 restraints weight = 21672.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.132969 restraints weight = 24624.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9120  Z= 0.328
  Angle     :  0.660  11.286  12359  Z= 0.347
  Chirality :  0.045   0.177   1389
  Planarity :  0.004   0.054   1580
  Dihedral  :  5.248  23.608   1247
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.44 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.24), residues: 1129
  helix: -1.29 (0.25), residues: 408
  sheet: -2.17 (0.35), residues: 207
  loop : -2.25 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R 297 
 HIS   0.006   0.001   HIS G  44 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.015   0.002   TYR R 220 
 ARG   0.004   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.982 
Fit side-chains
REVERT: R  230 PHE cc_start: 0.7064 (m-10) cc_final: 0.6532 (t80)
REVERT: R  345 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6147 (tp)
REVERT: R  351 LYS cc_start: 0.7664 (tptt) cc_final: 0.6823 (tttt)
  outliers start: 26
  outliers final: 21
  residues processed: 120
  average time/residue: 0.2176
  time to fit residues: 36.2966
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  298 THR
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Chi-restraints excluded: chain R residue  366 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0570
   chunk 61 optimal weight:    0.1980
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 240 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.168173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144010 restraints weight = 10603.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.141411 restraints weight = 21531.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.138808 restraints weight = 22105.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9120  Z= 0.141
  Angle     :  0.555  12.670  12359  Z= 0.287
  Chirality :  0.040   0.156   1389
  Planarity :  0.004   0.051   1580
  Dihedral  :  4.565  23.559   1247
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.52 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.24), residues: 1129
  helix: -0.88 (0.26), residues: 411
  sheet: -1.95 (0.36), residues: 195
  loop : -2.00 (0.25), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.019   0.001   PHE R 280 
 TYR   0.015   0.001   TYR R 291 
 ARG   0.003   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A  314 GLU cc_start: 0.6308 (tm-30) cc_final: 0.6044 (tm-30)
REVERT: B  129 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7168 (ttp80)
REVERT: R  230 PHE cc_start: 0.6906 (m-10) cc_final: 0.6384 (t80)
REVERT: R  345 ILE cc_start: 0.6439 (OUTLIER) cc_final: 0.6061 (tp)
  outliers start: 17
  outliers final: 13
  residues processed: 116
  average time/residue: 0.2293
  time to fit residues: 36.4836
Evaluate side-chains
  114 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  147 ILE
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 93 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 105 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.163635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.137947 restraints weight = 10677.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.131476 restraints weight = 19752.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.126403 restraints weight = 19793.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9120  Z= 0.206
  Angle     :  0.583  11.929  12359  Z= 0.304
  Chirality :  0.042   0.161   1389
  Planarity :  0.004   0.051   1580
  Dihedral  :  4.636  22.561   1247
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.95 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.24), residues: 1129
  helix: -0.79 (0.26), residues: 411
  sheet: -1.77 (0.36), residues: 203
  loop : -2.05 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 297 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.019   0.001   PHE N 108 
 TYR   0.014   0.001   TYR R 291 
 ARG   0.002   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.908 
Fit side-chains
REVERT: A  270 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8593 (mm)
REVERT: A  314 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6097 (tm-30)
REVERT: B   17 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7298 (tt0)
REVERT: B  129 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7187 (ttp80)
REVERT: R  230 PHE cc_start: 0.6997 (m-10) cc_final: 0.6359 (t80)
REVERT: R  345 ILE cc_start: 0.6341 (OUTLIER) cc_final: 0.5927 (tp)
  outliers start: 19
  outliers final: 15
  residues processed: 114
  average time/residue: 0.2258
  time to fit residues: 35.3525
Evaluate side-chains
  115 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 79 optimal weight:   50.0000
   chunk 85 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 111 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 83 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0570
   chunk 102 optimal weight:    0.7980
   overall best weight:    1.6502

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.163111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136935 restraints weight = 10629.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.134014 restraints weight = 20590.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.129744 restraints weight = 22215.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9120  Z= 0.215
  Angle     :  0.599  11.437  12359  Z= 0.311
  Chirality :  0.042   0.164   1389
  Planarity :  0.004   0.051   1580
  Dihedral  :  4.721  23.066   1247
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.49 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.24), residues: 1129
  helix: -0.79 (0.26), residues: 411
  sheet: -1.78 (0.36), residues: 203
  loop : -2.07 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 297 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.019   0.002   PHE N 108 
 TYR   0.013   0.001   TYR R 291 
 ARG   0.003   0.000   ARG A 228 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A  270 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8644 (mm)
REVERT: A  314 GLU cc_start: 0.6359 (tm-30) cc_final: 0.6045 (tm-30)
REVERT: B   17 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7270 (tt0)
REVERT: B  129 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7182 (ttp80)
REVERT: N   43 LYS cc_start: 0.7754 (tppp) cc_final: 0.7518 (tppt)
REVERT: R  230 PHE cc_start: 0.7012 (m-10) cc_final: 0.6384 (t80)
REVERT: R  345 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5920 (tp)
  outliers start: 18
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2316
  time to fit residues: 35.8270
Evaluate side-chains
  116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  155 ASN
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue   12 VAL
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  150 VAL
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0070
   chunk 111 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.167016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.143498 restraints weight = 10550.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141390 restraints weight = 22046.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.134699 restraints weight = 22624.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9120  Z= 0.141
  Angle     :  0.554  12.855  12359  Z= 0.286
  Chirality :  0.040   0.152   1389
  Planarity :  0.004   0.049   1580
  Dihedral  :  4.319  22.478   1247
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.93 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.25), residues: 1129
  helix: -0.48 (0.26), residues: 414
  sheet: -1.60 (0.34), residues: 215
  loop : -1.93 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 234 
 HIS   0.001   0.000   HIS B  91 
 PHE   0.018   0.001   PHE R 280 
 TYR   0.020   0.001   TYR N  80 
 ARG   0.003   0.000   ARG B  19 

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

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

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2258 Ramachandran restraints generated.
    1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A  270 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8534 (mm)
REVERT: A  314 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5951 (tm-30)
REVERT: B   17 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7286 (tt0)
REVERT: B  129 ARG cc_start: 0.7433 (ttp80) cc_final: 0.7111 (ttp80)
REVERT: R  230 PHE cc_start: 0.6924 (m-10) cc_final: 0.6410 (t80)
REVERT: R  345 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5794 (tp)
  outliers start: 16
  outliers final: 12
  residues processed: 117
  average time/residue: 0.2295
  time to fit residues: 36.7340
Evaluate side-chains
  116 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain G residue   22 GLU
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  195 PHE
Chi-restraints excluded: chain R residue  300 ASN
Chi-restraints excluded: chain R residue  307 LEU
Chi-restraints excluded: chain R residue  345 ILE
Chi-restraints excluded: chain R residue  357 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 76 optimal weight:   10.0000
   chunk 95 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0070
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.6400

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.168090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.143855 restraints weight = 10448.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141808 restraints weight = 21332.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136579 restraints weight = 22777.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9120  Z= 0.146
  Angle     :  0.549  12.446  12359  Z= 0.284
  Chirality :  0.040   0.158   1389
  Planarity :  0.003   0.049   1580
  Dihedral  :  4.123  21.080   1247
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.47 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.25), residues: 1129
  helix: -0.20 (0.27), residues: 408
  sheet: -1.34 (0.34), residues: 218
  loop : -1.79 (0.27), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 297 
 HIS   0.003   0.001   HIS G  44 
 PHE   0.017   0.001   PHE R 280 
 TYR   0.023   0.001   TYR N  80 
 ARG   0.003   0.000   ARG B  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2809.54 seconds
wall clock time: 49 minutes 31.25 seconds (2971.25 seconds total)