Starting phenix.real_space_refine
on Wed Apr 30 08:43:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nbi_0412/04_2025/6nbi_0412.cif"
  }
  resolution = 4.0
  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=   0.003
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      57      5.16       5
     C    5875      2.51       5
     N    1599      2.21       5
     O    1664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9195
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 3020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 3020
          Classifications: {'peptide': 369}
          Link IDs: {'PTRANS': 10, 'TRANS': 358}
          Chain breaks: 4
    Chain: "P"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 253
          Classifications: {'peptide': 30}
          Link IDs: {'TRANS': 29}
    Chain: "A"
      Number of atoms: 1840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1840
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "R"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 84
          Unusual residues: {'CLR': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.78, per 1000 atoms: 0.63
  Number of scatterers: 9195
  At special positions: 0
  Unit cell: (127.764, 99.372, 148.044, 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      57     16.00
     O    1664      8.00
     N    1599      7.00
     C    5875      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " distance=2.03
    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

  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: 2.44
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      41.1% alpha, 18.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'R' and resid 32 through 53
      removed outlier: 4.162A  pdb=" N   GLU R  36 " --> pdb=" O   MET R  32 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 173 through 201
      removed outlier: 3.878A  pdb=" N   GLU R 182 " --> pdb=" O   THR R 178 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL R 183 " --> pdb=" O   ARG R 179 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE R 184 " --> pdb=" O   GLU R 180 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASP R 185 " --> pdb=" O   ARG R 181 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   ARG R 186 " --> pdb=" O   GLU R 182 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU R 187 " --> pdb=" O   VAL R 183 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   TYR R 191 " --> pdb=" O   LEU R 187 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   THR R 192 " --> pdb=" O   ALA R 188 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU R 199 " --> pdb=" O   TYR R 195 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 212
    Processing helix  chain 'R' and resid 218 through 250
      removed outlier: 3.793A  pdb=" N   MET R 224 " --> pdb=" O   ASN R 220 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS R 240 " --> pdb=" O   SER R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 274 through 313
      removed outlier: 4.227A  pdb=" N   ALA R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ASN R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   TYR R 296 " --> pdb=" O   LEU R 292 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE R 310 " --> pdb=" O   LEU R 306 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE R 311 " --> pdb=" O   HIS R 307 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      removed outlier: 4.153A  pdb=" N   LEU R 331 " --> pdb=" O   PHE R 327 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
      removed outlier: 3.629A  pdb=" N   PHE R 335 " --> pdb=" O   LEU R 331 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 357 through 359
      No H-bonds generated for 'chain 'R' and resid 357 through 359'
    Processing helix  chain 'R' and resid 360 through 369
      removed outlier: 3.546A  pdb=" N   GLN R 364 " --> pdb=" O   LYS R 360 " (cutoff:3.500A)
      Proline residue:  R 366  - end of helix
    Processing helix  chain 'R' and resid 371 through 395
      removed outlier: 3.708A  pdb=" N   VAL R 384 " --> pdb=" O   ASN R 380 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   THR R 392 " --> pdb=" O   LYS R 388 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA R 394 " --> pdb=" O   ARG R 390 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY R 395 " --> pdb=" O   GLU R 391 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 400 through 412
    Processing helix  chain 'R' and resid 419 through 424
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 4.747A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR R 459 " --> pdb=" O   VAL R 455 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 481
    Processing helix  chain 'P' and resid 2 through 16
    Processing helix  chain 'P' and resid 17 through 25
      removed outlier: 3.932A  pdb=" N   ARG P  21 " --> pdb=" O   ASP P  17 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS P  25 " --> pdb=" O   ARG P  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.667A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ARG A  20 " --> pdb=" O   GLU A  16 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 3.725A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.502A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.797A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 4.099A  pdb=" N   ASP A 381 " --> pdb=" O   ASN A 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.636A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.515A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   MET G  38 " --> pdb=" O   ALA G  34 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.025A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 213
      removed outlier: 3.591A  pdb=" N   HIS A  41 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   HIS A 220 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.181A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.133A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.133A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.769A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.866A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.534A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 178 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.660A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.595A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.626A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.819A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER N  49 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    421 hydrogen bonds defined for protein.
    1206 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: 2.59

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2960
        1.35 -     1.47: 2312
        1.47 -     1.59: 4051
        1.59 -     1.71: 0
        1.71 -     1.83: 80
  Bond restraints: 9403
  Sorted by residual:
  bond pdb=" C   THR A 320 "
       pdb=" N   PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.330  1.361 -0.031 1.19e-02 7.06e+03 6.81e+00
  bond pdb=" C   MET R 414 "
       pdb=" N   PRO R 415 "
    ideal  model  delta    sigma   weight residual
    1.336  1.363 -0.027 1.23e-02 6.61e+03 4.91e+00
  bond pdb=" C   PHE A 312 "
       pdb=" O   PHE A 312 "
    ideal  model  delta    sigma   weight residual
    1.249  1.232  0.017 8.50e-03 1.38e+04 4.05e+00
  bond pdb=" C   ALA R 122 "
       pdb=" N   PRO R 123 "
    ideal  model  delta    sigma   weight residual
    1.331  1.354 -0.022 1.20e-02 6.94e+03 3.50e+00
  bond pdb=" CA  VAL B  40 "
       pdb=" C   VAL B  40 "
    ideal  model  delta    sigma   weight residual
    1.518  1.539 -0.021 1.13e-02 7.83e+03 3.36e+00
  ... (remaining 9398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 11283
        1.33 -     2.66: 1286
        2.66 -     3.99: 150
        3.99 -     5.32: 25
        5.32 -     6.65: 2
  Bond angle restraints: 12746
  Sorted by residual:
  angle pdb=" C   ASP A 354 "
        pdb=" N   GLY A 355 "
        pdb=" CA  GLY A 355 "
      ideal   model   delta    sigma   weight residual
     119.98  124.68   -4.70 1.11e+00 8.12e-01 1.79e+01
  angle pdb=" N   VAL R 171 "
        pdb=" CA  VAL R 171 "
        pdb=" C   VAL R 171 "
      ideal   model   delta    sigma   weight residual
     106.21  109.86   -3.65 1.07e+00 8.73e-01 1.17e+01
  angle pdb=" C   THR N  61 "
        pdb=" N   GLY N  62 "
        pdb=" CA  GLY N  62 "
      ideal   model   delta    sigma   weight residual
     120.03  123.78   -3.75 1.12e+00 7.97e-01 1.12e+01
  angle pdb=" C   GLU A 370 "
        pdb=" N   ASN A 371 "
        pdb=" CA  ASN A 371 "
      ideal   model   delta    sigma   weight residual
     120.38  124.88   -4.50 1.37e+00 5.33e-01 1.08e+01
  angle pdb=" C   GLN R 451 "
        pdb=" N   GLY R 452 "
        pdb=" CA  GLY R 452 "
      ideal   model   delta    sigma   weight residual
     119.99  123.65   -3.66 1.13e+00 7.83e-01 1.05e+01
  ... (remaining 12741 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.33: 5337
       13.33 -    26.67: 297
       26.67 -    40.00: 53
       40.00 -    53.33: 15
       53.33 -    66.66: 6
  Dihedral angle restraints: 5708
    sinusoidal: 2391
      harmonic: 3317
  Sorted by residual:
  dihedral pdb=" CB  CYS R 281 "
           pdb=" SG  CYS R 281 "
           pdb=" SG  CYS R 351 "
           pdb=" CB  CYS R 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.92  -41.92     1      1.00e+01 1.00e-02 2.46e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.20   17.80     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  LEU R 289 "
           pdb=" C   LEU R 289 "
           pdb=" N   TYR R 290 "
           pdb=" CA  TYR R 290 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.29   17.71     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 5705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 871
       0.046 -    0.091: 428
       0.091 -    0.137: 97
       0.137 -    0.183: 19
       0.183 -    0.228: 1
  Chirality restraints: 1416
  Sorted by residual:
  chirality pdb=" C14 CLR R 602 "
            pdb=" C13 CLR R 602 "
            pdb=" C15 CLR R 602 "
            pdb=" C8  CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.55    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" C10 CLR R 603 "
            pdb=" C1  CLR R 603 "
            pdb=" C5  CLR R 603 "
            pdb=" C9  CLR R 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.67   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality pdb=" C10 CLR R 602 "
            pdb=" C1  CLR R 602 "
            pdb=" C5  CLR R 602 "
            pdb=" C9  CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.67   -0.18 2.00e-01 2.50e+01 7.86e-01
  ... (remaining 1413 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R  34 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.38e+00
        pdb=" C   LYS R  34 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LYS R  34 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU R  35 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "   -0.032 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO G  49 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  32 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.91e+00
        pdb=" C   LYS A  32 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS A  32 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A  33 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2845
        2.85 -     3.36: 7823
        3.36 -     3.87: 14237
        3.87 -     4.39: 16041
        4.39 -     4.90: 28235
  Nonbonded interactions: 69181
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R 421 "
            pdb=" OE1 GLN R 451 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   MET R 425 "
            pdb=" N   ALA P   1 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" O   SER R 341 "
            pdb=" OG1 THR R 345 "
     model   vdw
     2.390 3.040
  ... (remaining 69176 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.380
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   9409  Z= 0.363
  Angle     :  0.880   7.200  12758  Z= 0.594
  Chirality :  0.053   0.228   1416
  Planarity :  0.004   0.068   1604
  Dihedral  :  8.927  66.664   3544
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.72 %
    Favored  : 98.97 %
  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: -1.70 (0.22), residues: 1115
  helix: -0.65 (0.22), residues: 447
  sheet: -0.86 (0.33), residues: 217
  loop : -1.61 (0.25), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 154 
 HIS   0.006   0.001   HIS A 387 
 PHE   0.014   0.002   PHE R 447 
 TYR   0.025   0.002   TYR R 191 
 ARG   0.003   0.000   ARG A 389 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17252 (  421)
  hydrogen bonds       : angle       7.22663 ( 1206)
  SS BOND              : bond        0.00647 (    6)
  SS BOND              : angle       2.78457 (   12)
  covalent geometry    : bond        0.00525 ( 9403)
  covalent geometry    : angle       0.87594 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  531 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 528
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  307 HIS cc_start: 0.8222 (t-90) cc_final: 0.7726 (t-90)
REVERT: R  445 MET cc_start: 0.8003 (mmp) cc_final: 0.7612 (mmp)
REVERT: A   13 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7537 (mpt180)
REVERT: A   16 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8821 (pt0)
REVERT: A  278 ASN cc_start: 0.8348 (m110) cc_final: 0.7768 (m-40)
REVERT: A  286 SER cc_start: 0.9489 (t) cc_final: 0.9265 (p)
REVERT: B   10 GLU cc_start: 0.9371 (tt0) cc_final: 0.9099 (tm-30)
REVERT: B   20 ASP cc_start: 0.9095 (m-30) cc_final: 0.8651 (m-30)
REVERT: B   51 LEU cc_start: 0.7980 (mt) cc_final: 0.7775 (mp)
REVERT: B  184 THR cc_start: 0.8195 (p) cc_final: 0.7920 (t)
REVERT: B  301 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7861 (mmtp)
REVERT: B  316 SER cc_start: 0.8935 (p) cc_final: 0.8730 (t)
REVERT: G   38 MET cc_start: 0.9299 (mtm) cc_final: 0.9086 (mtt)
REVERT: N   77 ASN cc_start: 0.9057 (m-40) cc_final: 0.8783 (t0)
REVERT: N  122 THR cc_start: 0.7406 (t) cc_final: 0.6816 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 530
  average time/residue: 0.2697
  time to fit residues: 184.2817
Evaluate side-chains
  302 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 300
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain B residue  234 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    0.3980
   chunk 44 optimal weight:    8.9990
   chunk 87 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0370
   chunk 64 optimal weight:    0.0470
   chunk 100 optimal weight:   20.0000
   overall best weight:    1.2960

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

Flipped N/Q/H residues before XYZ refinement:
R 295 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 438 GLN
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  25 HIS
B 156 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.113156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.090147 restraints weight = 30268.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.092506 restraints weight = 19883.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.094112 restraints weight = 14579.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9409  Z= 0.148
  Angle     :  0.683  10.185  12758  Z= 0.355
  Chirality :  0.044   0.353   1416
  Planarity :  0.005   0.045   1604
  Dihedral  :  5.497  43.356   1449
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.98 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.24), residues: 1115
  helix:  1.05 (0.25), residues: 437
  sheet: -0.28 (0.32), residues: 224
  loop : -1.20 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  14 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.012   0.001   PHE R 315 
 TYR   0.013   0.002   TYR N  32 
 ARG   0.008   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04605 (  421)
  hydrogen bonds       : angle       5.21441 ( 1206)
  SS BOND              : bond        0.00605 (    6)
  SS BOND              : angle       2.00817 (   12)
  covalent geometry    : bond        0.00318 ( 9403)
  covalent geometry    : angle       0.68024 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 323
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  364 GLN cc_start: 0.9411 (tp40) cc_final: 0.9187 (tp40)
REVERT: R  438 GLN cc_start: 0.7763 (pt0) cc_final: 0.7551 (pt0)
REVERT: A   17 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8878 (mmtt)
REVERT: A  218 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7995 (p0)
REVERT: A  240 ASP cc_start: 0.8543 (p0) cc_final: 0.8089 (p0)
REVERT: A  264 ASN cc_start: 0.8383 (t0) cc_final: 0.8152 (t0)
REVERT: A  340 PHE cc_start: 0.8717 (t80) cc_final: 0.8381 (t80)
REVERT: B   12 GLU cc_start: 0.8972 (tp30) cc_final: 0.8772 (tp30)
REVERT: B   16 ASN cc_start: 0.9359 (m-40) cc_final: 0.8923 (m-40)
REVERT: B   51 LEU cc_start: 0.9567 (mt) cc_final: 0.9184 (mp)
REVERT: B  184 THR cc_start: 0.8644 (p) cc_final: 0.8114 (t)
REVERT: B  252 LEU cc_start: 0.9737 (tp) cc_final: 0.9512 (tt)
REVERT: B  275 SER cc_start: 0.9462 (t) cc_final: 0.9258 (m)
REVERT: B  308 LEU cc_start: 0.9046 (mp) cc_final: 0.8788 (tp)
REVERT: G   11 GLN cc_start: 0.8791 (pt0) cc_final: 0.8462 (pp30)
REVERT: N   20 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.6210 (mt)
REVERT: N   38 ARG cc_start: 0.8714 (ptt180) cc_final: 0.8456 (ptm160)
REVERT: N   81 LEU cc_start: 0.6778 (tp) cc_final: 0.6290 (tt)
  outliers start: 39
  outliers final: 22
  residues processed: 346
  average time/residue: 0.2358
  time to fit residues: 109.5348
Evaluate side-chains
  292 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 268
  time to evaluate  : 1.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  288 PHE
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  388 LYS
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   93 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0570
   chunk 94 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    0.9300

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

Flipped N/Q/H residues before XYZ refinement:
R 295 ASN
R 307 HIS
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P   6 GLN
** P  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  14 ASN
A  19 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 ASN
B 220 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.117653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.096616 restraints weight = 29369.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.098595 restraints weight = 19817.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.100015 restraints weight = 14939.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9409  Z= 0.127
  Angle     :  0.635  10.497  12758  Z= 0.326
  Chirality :  0.043   0.327   1416
  Planarity :  0.004   0.059   1604
  Dihedral  :  5.141  46.788   1449
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.75 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1115
  helix:  1.23 (0.25), residues: 431
  sheet: -0.06 (0.31), residues: 244
  loop : -1.00 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.015   0.001   HIS P   9 
 PHE   0.015   0.001   PHE R 378 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.009   0.001   ARG P  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (  421)
  hydrogen bonds       : angle       5.04508 ( 1206)
  SS BOND              : bond        0.00459 (    6)
  SS BOND              : angle       1.63544 (   12)
  covalent geometry    : bond        0.00280 ( 9403)
  covalent geometry    : angle       0.63335 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 287
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  440 GLN cc_start: 0.9024 (pp30) cc_final: 0.8414 (pp30)
REVERT: R  442 HIS cc_start: 0.8329 (m90) cc_final: 0.8069 (m90)
REVERT: R  445 MET cc_start: 0.7718 (mmp) cc_final: 0.6767 (mmp)
REVERT: A  240 ASP cc_start: 0.8526 (p0) cc_final: 0.7967 (p0)
REVERT: A  270 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9506 (mm)
REVERT: A  360 TYR cc_start: 0.8548 (m-80) cc_final: 0.8102 (m-80)
REVERT: B    6 GLN cc_start: 0.9405 (pp30) cc_final: 0.9109 (pm20)
REVERT: B   12 GLU cc_start: 0.8907 (tp30) cc_final: 0.8654 (tp30)
REVERT: B  124 TYR cc_start: 0.8906 (m-80) cc_final: 0.8519 (m-80)
REVERT: B  184 THR cc_start: 0.8474 (p) cc_final: 0.7897 (t)
REVERT: G   11 GLN cc_start: 0.8892 (pt0) cc_final: 0.8538 (pp30)
REVERT: N    4 LEU cc_start: 0.8813 (mm) cc_final: 0.8517 (mm)
REVERT: N   20 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6274 (mp)
REVERT: N   50 ASP cc_start: 0.8759 (p0) cc_final: 0.8433 (p0)
REVERT: N   81 LEU cc_start: 0.6645 (tp) cc_final: 0.6159 (tt)
REVERT: N  122 THR cc_start: 0.7957 (t) cc_final: 0.7600 (t)
  outliers start: 37
  outliers final: 27
  residues processed: 306
  average time/residue: 0.2210
  time to fit residues: 92.3526
Evaluate side-chains
  278 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 249
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  288 PHE
Chi-restraints excluded: chain R residue  374 ASN
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  449 SER
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain P residue    5 ILE
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   83 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 93 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 6 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
R 225 HIS
R 295 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 GLN
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
A 271 ASN
B 142 HIS
G  18 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.110615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088062 restraints weight = 31260.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.090150 restraints weight = 21129.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.091480 restraints weight = 15988.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.6873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9409  Z= 0.219
  Angle     :  0.696  11.022  12758  Z= 0.366
  Chirality :  0.043   0.250   1416
  Planarity :  0.005   0.048   1604
  Dihedral  :  5.263  49.594   1449
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 20.37 %
    Favored  : 72.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.25), residues: 1115
  helix:  0.93 (0.24), residues: 444
  sheet: -0.01 (0.31), residues: 239
  loop : -0.99 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R 352 
 HIS   0.020   0.001   HIS P   9 
 PHE   0.035   0.002   PHE R 184 
 TYR   0.017   0.002   TYR A 358 
 ARG   0.010   0.001   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04503 (  421)
  hydrogen bonds       : angle       5.24754 ( 1206)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       1.86386 (   12)
  covalent geometry    : bond        0.00475 ( 9403)
  covalent geometry    : angle       0.69439 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 266
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  237 ILE cc_start: 0.9416 (mm) cc_final: 0.9143 (mm)
REVERT: R  241 ASP cc_start: 0.8439 (m-30) cc_final: 0.8203 (p0)
REVERT: R  306 LEU cc_start: 0.9549 (tp) cc_final: 0.9264 (tt)
REVERT: R  364 GLN cc_start: 0.9066 (tp40) cc_final: 0.8770 (tp40)
REVERT: R  367 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9017 (tp)
REVERT: P    2 VAL cc_start: 0.9638 (t) cc_final: 0.9308 (m)
REVERT: A  240 ASP cc_start: 0.8719 (p0) cc_final: 0.7978 (p0)
REVERT: A  365 CYS cc_start: 0.7995 (t) cc_final: 0.7583 (m)
REVERT: A  386 MET cc_start: 0.8640 (tmm) cc_final: 0.8421 (tmm)
REVERT: B    6 GLN cc_start: 0.9457 (pp30) cc_final: 0.9166 (pm20)
REVERT: B   12 GLU cc_start: 0.8931 (tp30) cc_final: 0.8465 (tp30)
REVERT: B   15 LYS cc_start: 0.9399 (ptpt) cc_final: 0.9156 (ptpt)
REVERT: B  124 TYR cc_start: 0.8715 (m-80) cc_final: 0.8432 (m-80)
REVERT: B  127 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8898 (ptmm)
REVERT: B  215 GLU cc_start: 0.8919 (mp0) cc_final: 0.8135 (mp0)
REVERT: B  339 TRP cc_start: 0.7963 (m100) cc_final: 0.7412 (m100)
REVERT: G   11 GLN cc_start: 0.8909 (pt0) cc_final: 0.8543 (pp30)
REVERT: N    4 LEU cc_start: 0.8910 (mm) cc_final: 0.8618 (mm)
REVERT: N   19 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7181 (ttp80)
REVERT: N   50 ASP cc_start: 0.8891 (p0) cc_final: 0.8611 (p0)
REVERT: N   81 LEU cc_start: 0.6902 (tp) cc_final: 0.6630 (tt)
REVERT: N   90 ASP cc_start: 0.7860 (m-30) cc_final: 0.7465 (m-30)
REVERT: N   91 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7573 (t)
  outliers start: 67
  outliers final: 45
  residues processed: 304
  average time/residue: 0.2102
  time to fit residues: 87.5910
Evaluate side-chains
  280 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 233
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  145 TYR
Chi-restraints excluded: chain R residue  218 THR
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  288 PHE
Chi-restraints excluded: chain R residue  289 LEU
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain R residue  381 ILE
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  449 SER
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   18 GLN
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 63 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 105 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 236 GLN
** G  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.114755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.091504 restraints weight = 32152.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.093735 restraints weight = 21303.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.095194 restraints weight = 15907.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.7188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9409  Z= 0.134
  Angle     :  0.655  10.126  12758  Z= 0.341
  Chirality :  0.043   0.304   1416
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.892  50.529   1449
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 22.74 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.25), residues: 1115
  helix:  1.18 (0.25), residues: 435
  sheet:  0.30 (0.32), residues: 229
  loop : -0.96 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 437 
 HIS   0.017   0.001   HIS P   9 
 PHE   0.023   0.002   PHE R 184 
 TYR   0.021   0.001   TYR R 421 
 ARG   0.005   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  421)
  hydrogen bonds       : angle       4.98162 ( 1206)
  SS BOND              : bond        0.00225 (    6)
  SS BOND              : angle       1.30596 (   12)
  covalent geometry    : bond        0.00297 ( 9403)
  covalent geometry    : angle       0.65426 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 258
  time to evaluate  : 1.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  220 ASN cc_start: 0.9220 (m-40) cc_final: 0.8965 (m-40)
REVERT: R  237 ILE cc_start: 0.9515 (mm) cc_final: 0.9199 (mm)
REVERT: R  324 PHE cc_start: 0.8598 (m-80) cc_final: 0.8311 (m-80)
REVERT: R  364 GLN cc_start: 0.9006 (tp40) cc_final: 0.8723 (tp40)
REVERT: R  368 LEU cc_start: 0.9326 (mm) cc_final: 0.9058 (mm)
REVERT: R  440 GLN cc_start: 0.9112 (pp30) cc_final: 0.8772 (pp30)
REVERT: R  467 GLN cc_start: 0.8427 (mt0) cc_final: 0.8073 (mt0)
REVERT: P    2 VAL cc_start: 0.9438 (t) cc_final: 0.9121 (m)
REVERT: P    6 GLN cc_start: 0.8653 (tp40) cc_final: 0.8008 (tp40)
REVERT: P   10 GLN cc_start: 0.8708 (pp30) cc_final: 0.8424 (pp30)
REVERT: A  240 ASP cc_start: 0.8704 (p0) cc_final: 0.7956 (p0)
REVERT: A  365 CYS cc_start: 0.8077 (t) cc_final: 0.7580 (m)
REVERT: A  386 MET cc_start: 0.8720 (tmm) cc_final: 0.8441 (tmm)
REVERT: B    6 GLN cc_start: 0.9466 (pp30) cc_final: 0.9143 (pm20)
REVERT: B    8 ARG cc_start: 0.7652 (mpp80) cc_final: 0.7443 (mpp80)
REVERT: B   12 GLU cc_start: 0.8954 (tp30) cc_final: 0.8271 (tp30)
REVERT: B   15 LYS cc_start: 0.9416 (ptpt) cc_final: 0.9055 (pttp)
REVERT: B   16 ASN cc_start: 0.9290 (m-40) cc_final: 0.8783 (m-40)
REVERT: B  215 GLU cc_start: 0.8789 (mp0) cc_final: 0.8169 (mp0)
REVERT: G   11 GLN cc_start: 0.8920 (pt0) cc_final: 0.8560 (pp30)
REVERT: G   17 GLU cc_start: 0.9059 (pp20) cc_final: 0.8656 (pp20)
REVERT: N    4 LEU cc_start: 0.8870 (mm) cc_final: 0.8489 (mm)
REVERT: N   50 ASP cc_start: 0.8859 (p0) cc_final: 0.8546 (p0)
REVERT: N   81 LEU cc_start: 0.7055 (tp) cc_final: 0.6689 (tt)
REVERT: N   91 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7342 (t)
  outliers start: 57
  outliers final: 40
  residues processed: 294
  average time/residue: 0.2238
  time to fit residues: 90.5688
Evaluate side-chains
  284 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 243
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  189 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  449 SER
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 72 optimal weight:    0.1980
   chunk 31 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 295 ASN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  10 GLN
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.114495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.091531 restraints weight = 30983.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.093674 restraints weight = 20769.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.095019 restraints weight = 15713.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.7402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9409  Z= 0.120
  Angle     :  0.655   9.172  12758  Z= 0.339
  Chirality :  0.042   0.252   1416
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.743  51.569   1449
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 22.94 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1115
  helix:  1.22 (0.25), residues: 437
  sheet:  0.23 (0.33), residues: 225
  loop : -0.89 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 322 
 HIS   0.016   0.001   HIS P   9 
 PHE   0.020   0.001   PHE R 184 
 TYR   0.019   0.001   TYR R 245 
 ARG   0.010   0.001   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  421)
  hydrogen bonds       : angle       4.76844 ( 1206)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       1.08997 (   12)
  covalent geometry    : bond        0.00261 ( 9403)
  covalent geometry    : angle       0.65459 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 265
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  177 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: R  220 ASN cc_start: 0.9144 (m-40) cc_final: 0.8864 (m-40)
REVERT: R  324 PHE cc_start: 0.8558 (m-80) cc_final: 0.8226 (m-80)
REVERT: R  467 GLN cc_start: 0.8532 (mt0) cc_final: 0.8183 (mt0)
REVERT: A  240 ASP cc_start: 0.8599 (p0) cc_final: 0.7893 (p0)
REVERT: A  365 CYS cc_start: 0.8236 (t) cc_final: 0.7644 (m)
REVERT: A  386 MET cc_start: 0.8780 (tmm) cc_final: 0.8480 (tmm)
REVERT: B    6 GLN cc_start: 0.9427 (pp30) cc_final: 0.9096 (pm20)
REVERT: B   12 GLU cc_start: 0.8996 (tp30) cc_final: 0.8426 (tp30)
REVERT: B   15 LYS cc_start: 0.9454 (ptpt) cc_final: 0.9083 (pttp)
REVERT: B   16 ASN cc_start: 0.9316 (m-40) cc_final: 0.8829 (m-40)
REVERT: B  215 GLU cc_start: 0.8911 (mp0) cc_final: 0.8177 (mp0)
REVERT: G   11 GLN cc_start: 0.8841 (pt0) cc_final: 0.8508 (pp30)
REVERT: N    4 LEU cc_start: 0.8848 (mm) cc_final: 0.8354 (mm)
REVERT: N    5 GLN cc_start: 0.8276 (tp40) cc_final: 0.7945 (tp40)
  outliers start: 52
  outliers final: 41
  residues processed: 298
  average time/residue: 0.2034
  time to fit residues: 84.1971
Evaluate side-chains
  274 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 233
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  140 HIS
Chi-restraints excluded: chain R residue  189 MET
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 96 optimal weight:    0.0870
   chunk 84 optimal weight:    6.9990
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
R  37 GLN
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.111207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088416 restraints weight = 31012.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.090699 restraints weight = 19942.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.092231 restraints weight = 14681.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.7604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9409  Z= 0.124
  Angle     :  0.701  11.110  12758  Z= 0.358
  Chirality :  0.042   0.217   1416
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.629  52.061   1449
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.66 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1115
  helix:  1.25 (0.25), residues: 438
  sheet:  0.20 (0.34), residues: 225
  loop : -0.82 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 322 
 HIS   0.010   0.001   HIS P   9 
 PHE   0.021   0.001   PHE R 184 
 TYR   0.029   0.001   TYR R 191 
 ARG   0.007   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  421)
  hydrogen bonds       : angle       4.79846 ( 1206)
  SS BOND              : bond        0.00255 (    6)
  SS BOND              : angle       1.00853 (   12)
  covalent geometry    : bond        0.00279 ( 9403)
  covalent geometry    : angle       0.70057 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 253
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  177 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9000 (mm-30)
REVERT: R  220 ASN cc_start: 0.9075 (m-40) cc_final: 0.8816 (m-40)
REVERT: R  324 PHE cc_start: 0.8567 (m-80) cc_final: 0.8207 (m-80)
REVERT: R  364 GLN cc_start: 0.9058 (tp40) cc_final: 0.8721 (tp40)
REVERT: R  467 GLN cc_start: 0.8527 (mt0) cc_final: 0.8193 (mt0)
REVERT: P    2 VAL cc_start: 0.9436 (t) cc_final: 0.9159 (m)
REVERT: P    6 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8041 (mp10)
REVERT: A  240 ASP cc_start: 0.8583 (p0) cc_final: 0.7864 (p0)
REVERT: A  270 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9428 (mm)
REVERT: A  360 TYR cc_start: 0.8191 (m-80) cc_final: 0.7835 (m-80)
REVERT: A  365 CYS cc_start: 0.8237 (t) cc_final: 0.7599 (m)
REVERT: A  385 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8224 (mtp85)
REVERT: A  386 MET cc_start: 0.8792 (tmm) cc_final: 0.8514 (tmm)
REVERT: B   12 GLU cc_start: 0.8983 (tp30) cc_final: 0.8415 (tp30)
REVERT: B   15 LYS cc_start: 0.9442 (ptpt) cc_final: 0.9076 (pttp)
REVERT: B   16 ASN cc_start: 0.9302 (m-40) cc_final: 0.8813 (m-40)
REVERT: B  215 GLU cc_start: 0.8932 (mp0) cc_final: 0.8228 (mp0)
REVERT: B  337 LYS cc_start: 0.8931 (mmtm) cc_final: 0.8518 (mmmt)
REVERT: G   11 GLN cc_start: 0.8882 (pt0) cc_final: 0.8557 (pp30)
REVERT: G   21 MET cc_start: 0.8202 (tpt) cc_final: 0.7933 (ttm)
REVERT: N    4 LEU cc_start: 0.8772 (mm) cc_final: 0.8242 (mm)
REVERT: N    5 GLN cc_start: 0.8200 (tp40) cc_final: 0.7896 (tp40)
REVERT: N   90 ASP cc_start: 0.8157 (m-30) cc_final: 0.7560 (m-30)
  outliers start: 47
  outliers final: 40
  residues processed: 284
  average time/residue: 0.2074
  time to fit residues: 81.0609
Evaluate side-chains
  275 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 233
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  140 HIS
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue   11 ARG
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   25 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 68 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 3 optimal weight:   20.0000
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  25 HIS
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.110605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.088118 restraints weight = 32339.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.090169 restraints weight = 21760.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.091515 restraints weight = 16511.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.7971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9409  Z= 0.169
  Angle     :  0.732  11.795  12758  Z= 0.381
  Chirality :  0.044   0.213   1416
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.844  53.549   1449
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.07 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1115
  helix:  0.88 (0.24), residues: 450
  sheet:  0.03 (0.33), residues: 232
  loop : -0.95 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 322 
 HIS   0.009   0.001   HIS P   9 
 PHE   0.020   0.002   PHE R 227 
 TYR   0.021   0.002   TYR R 421 
 ARG   0.013   0.001   ARG B   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  421)
  hydrogen bonds       : angle       4.99506 ( 1206)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       1.24183 (   12)
  covalent geometry    : bond        0.00373 ( 9403)
  covalent geometry    : angle       0.73134 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 243
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  324 PHE cc_start: 0.8427 (m-80) cc_final: 0.8146 (m-80)
REVERT: R  467 GLN cc_start: 0.8502 (mt0) cc_final: 0.8251 (mt0)
REVERT: P    2 VAL cc_start: 0.9436 (t) cc_final: 0.9097 (m)
REVERT: P    6 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7928 (mp10)
REVERT: A   30 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9347 (tt)
REVERT: A  270 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9356 (mm)
REVERT: A  365 CYS cc_start: 0.8130 (t) cc_final: 0.7544 (m)
REVERT: A  386 MET cc_start: 0.8849 (tmm) cc_final: 0.8596 (tmm)
REVERT: B   12 GLU cc_start: 0.8899 (tp30) cc_final: 0.8675 (tp30)
REVERT: B   16 ASN cc_start: 0.9310 (m-40) cc_final: 0.8878 (m-40)
REVERT: B  215 GLU cc_start: 0.8874 (mp0) cc_final: 0.8204 (mp0)
REVERT: B  339 TRP cc_start: 0.8089 (m100) cc_final: 0.7617 (m100)
REVERT: G   11 GLN cc_start: 0.8890 (pt0) cc_final: 0.8547 (pp30)
REVERT: G   21 MET cc_start: 0.8194 (tpt) cc_final: 0.7829 (ttm)
REVERT: N    4 LEU cc_start: 0.8719 (mm) cc_final: 0.8204 (mm)
REVERT: N    5 GLN cc_start: 0.8076 (tp40) cc_final: 0.7841 (tp40)
REVERT: N   50 ASP cc_start: 0.8893 (p0) cc_final: 0.8662 (p0)
REVERT: N   90 ASP cc_start: 0.8180 (m-30) cc_final: 0.7704 (m-30)
REVERT: N   95 TYR cc_start: 0.8529 (m-80) cc_final: 0.8253 (m-80)
  outliers start: 56
  outliers final: 46
  residues processed: 278
  average time/residue: 0.2026
  time to fit residues: 78.1838
Evaluate side-chains
  277 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 228
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  135 ILE
Chi-restraints excluded: chain R residue  140 HIS
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  381 ILE
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  421 TYR
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain P residue    9 HIS
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   86 LEU
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 103 optimal weight:    8.9990
   chunk 94 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  25 HIS
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.108574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.086133 restraints weight = 30696.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.088297 restraints weight = 19800.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.089742 restraints weight = 14648.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.8132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9409  Z= 0.141
  Angle     :  0.760  12.672  12758  Z= 0.387
  Chirality :  0.044   0.319   1416
  Planarity :  0.004   0.049   1604
  Dihedral  :  4.716  53.903   1449
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 26.13 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1115
  helix:  1.02 (0.25), residues: 443
  sheet:  0.20 (0.34), residues: 230
  loop : -0.98 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP R 322 
 HIS   0.011   0.001   HIS P   9 
 PHE   0.025   0.002   PHE R 227 
 TYR   0.021   0.001   TYR R 421 
 ARG   0.014   0.001   ARG B   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  421)
  hydrogen bonds       : angle       4.93696 ( 1206)
  SS BOND              : bond        0.00291 (    6)
  SS BOND              : angle       1.59207 (   12)
  covalent geometry    : bond        0.00320 ( 9403)
  covalent geometry    : angle       0.75869 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 237
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  177 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8991 (mm-30)
REVERT: R  240 LYS cc_start: 0.9299 (tppt) cc_final: 0.9032 (tppt)
REVERT: R  324 PHE cc_start: 0.8378 (m-80) cc_final: 0.8089 (m-80)
REVERT: R  364 GLN cc_start: 0.8900 (tp40) cc_final: 0.8525 (tp40)
REVERT: R  368 LEU cc_start: 0.9420 (mm) cc_final: 0.9046 (mm)
REVERT: R  425 MET cc_start: 0.6566 (tpp) cc_final: 0.6069 (tpp)
REVERT: R  467 GLN cc_start: 0.8469 (mt0) cc_final: 0.8214 (mt0)
REVERT: P    2 VAL cc_start: 0.9421 (t) cc_final: 0.9021 (m)
REVERT: P    6 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7735 (mp10)
REVERT: A   43 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8562 (mm)
REVERT: A  270 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9367 (mm)
REVERT: A  278 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8111 (t0)
REVERT: A  365 CYS cc_start: 0.8203 (t) cc_final: 0.7549 (m)
REVERT: A  386 MET cc_start: 0.8936 (tmm) cc_final: 0.8619 (tmm)
REVERT: B   12 GLU cc_start: 0.8945 (tp30) cc_final: 0.8733 (tp30)
REVERT: B   16 ASN cc_start: 0.9306 (m-40) cc_final: 0.8885 (m-40)
REVERT: B  215 GLU cc_start: 0.8922 (mp0) cc_final: 0.8193 (mp0)
REVERT: B  339 TRP cc_start: 0.7975 (m100) cc_final: 0.7579 (m100)
REVERT: G   11 GLN cc_start: 0.8905 (pt0) cc_final: 0.8568 (pp30)
REVERT: G   21 MET cc_start: 0.8241 (tpt) cc_final: 0.7874 (ttm)
REVERT: N    4 LEU cc_start: 0.8700 (mm) cc_final: 0.8188 (mm)
REVERT: N   50 ASP cc_start: 0.8886 (p0) cc_final: 0.8625 (p0)
REVERT: N   90 ASP cc_start: 0.8272 (m-30) cc_final: 0.7620 (m-30)
REVERT: N   95 TYR cc_start: 0.8563 (m-80) cc_final: 0.8275 (m-80)
  outliers start: 48
  outliers final: 41
  residues processed: 270
  average time/residue: 0.2086
  time to fit residues: 78.0697
Evaluate side-chains
  271 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 226
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  140 HIS
Chi-restraints excluded: chain R residue  183 VAL
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  381 ILE
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  421 TYR
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0980
   chunk 38 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    2.4188

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  25 HIS
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.109539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.086795 restraints weight = 32508.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.088870 restraints weight = 21501.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.090301 restraints weight = 16251.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.8383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9409  Z= 0.179
  Angle     :  0.796  13.674  12758  Z= 0.405
  Chirality :  0.045   0.292   1416
  Planarity :  0.004   0.050   1604
  Dihedral  :  4.912  54.887   1447
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 26.54 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.25), residues: 1115
  helix:  0.89 (0.24), residues: 443
  sheet: -0.04 (0.34), residues: 234
  loop : -0.94 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 322 
 HIS   0.009   0.001   HIS P   9 
 PHE   0.026   0.002   PHE R 227 
 TYR   0.031   0.002   TYR R 191 
 ARG   0.011   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04430 (  421)
  hydrogen bonds       : angle       5.09169 ( 1206)
  SS BOND              : bond        0.00266 (    6)
  SS BOND              : angle       2.11413 (   12)
  covalent geometry    : bond        0.00406 ( 9403)
  covalent geometry    : angle       0.79398 (12746)

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 227
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  324 PHE cc_start: 0.8309 (m-80) cc_final: 0.8025 (m-80)
REVERT: R  342 VAL cc_start: 0.9147 (p) cc_final: 0.8925 (m)
REVERT: R  364 GLN cc_start: 0.8875 (tp40) cc_final: 0.8570 (tp40)
REVERT: R  467 GLN cc_start: 0.8493 (mt0) cc_final: 0.8241 (mt0)
REVERT: P    2 VAL cc_start: 0.9346 (t) cc_final: 0.9040 (m)
REVERT: P    6 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8003 (mp10)
REVERT: A  270 LEU cc_start: 0.9770 (OUTLIER) cc_final: 0.9375 (mm)
REVERT: A  278 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8213 (t0)
REVERT: A  317 ARG cc_start: 0.8622 (ptp90) cc_final: 0.8157 (ptt-90)
REVERT: A  365 CYS cc_start: 0.8169 (t) cc_final: 0.7544 (m)
REVERT: A  386 MET cc_start: 0.8966 (tmm) cc_final: 0.8662 (tmm)
REVERT: B   10 GLU cc_start: 0.9263 (tm-30) cc_final: 0.9036 (tm-30)
REVERT: B   12 GLU cc_start: 0.8960 (tp30) cc_final: 0.8718 (tp30)
REVERT: B   15 LYS cc_start: 0.9390 (ptpt) cc_final: 0.9123 (ptpp)
REVERT: B   16 ASN cc_start: 0.9267 (m-40) cc_final: 0.8925 (m-40)
REVERT: B  215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8207 (mp0)
REVERT: B  339 TRP cc_start: 0.7976 (m100) cc_final: 0.7506 (m100)
REVERT: G   11 GLN cc_start: 0.8862 (pt0) cc_final: 0.8517 (pp30)
REVERT: G   21 MET cc_start: 0.8311 (tpt) cc_final: 0.7896 (ttt)
REVERT: N    4 LEU cc_start: 0.8621 (mm) cc_final: 0.8141 (mm)
REVERT: N   50 ASP cc_start: 0.8923 (p0) cc_final: 0.8668 (p0)
REVERT: N   90 ASP cc_start: 0.8329 (m-30) cc_final: 0.7721 (m-30)
REVERT: N   95 TYR cc_start: 0.8609 (m-80) cc_final: 0.8325 (m-80)
  outliers start: 48
  outliers final: 43
  residues processed: 261
  average time/residue: 0.2053
  time to fit residues: 74.7654
Evaluate side-chains
  265 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 219
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   39 PHE
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  140 HIS
Chi-restraints excluded: chain R residue  183 VAL
Chi-restraints excluded: chain R residue  228 LEU
Chi-restraints excluded: chain R residue  231 MET
Chi-restraints excluded: chain R residue  354 LEU
Chi-restraints excluded: chain R residue  381 ILE
Chi-restraints excluded: chain R residue  385 LEU
Chi-restraints excluded: chain R residue  389 LEU
Chi-restraints excluded: chain R residue  407 LEU
Chi-restraints excluded: chain R residue  421 TYR
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  466 VAL
Chi-restraints excluded: chain R residue  481 LEU
Chi-restraints excluded: chain P residue    6 GLN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  278 ASN
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  344 GLU
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain G residue   26 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain N residue   96 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 31 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0970
   chunk 109 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0270
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0060
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.3454

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

Flipped N/Q/H residues before XYZ refinement:
** R 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 451 GLN
** P   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.110596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.088242 restraints weight = 31072.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.090500 restraints weight = 19832.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.092033 restraints weight = 14546.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.8425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9409  Z= 0.140
  Angle     :  0.817  12.415  12758  Z= 0.408
  Chirality :  0.045   0.314   1416
  Planarity :  0.004   0.089   1604
  Dihedral  :  4.683  54.479   1447
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 28.29 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.25), residues: 1115
  helix:  0.84 (0.25), residues: 443
  sheet:  0.08 (0.33), residues: 230
  loop : -0.98 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP R 322 
 HIS   0.014   0.001   HIS P   9 
 PHE   0.028   0.001   PHE R 227 
 TYR   0.020   0.001   TYR R 421 
 ARG   0.011   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03982 (  421)
  hydrogen bonds       : angle       4.94155 ( 1206)
  SS BOND              : bond        0.00206 (    6)
  SS BOND              : angle       1.55454 (   12)
  covalent geometry    : bond        0.00319 ( 9403)
  covalent geometry    : angle       0.81605 (12746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3546.86 seconds
wall clock time: 62 minutes 20.64 seconds (3740.64 seconds total)