Starting phenix.real_space_refine
on Thu Mar 13 02:24:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xvi_38705/03_2025/8xvi_38705.cif"
  }
  resolution = 3.32
  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=   0.001 sd=   0.028
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      67      5.16       5
     C    5449      2.51       5
     N    1484      2.21       5
     O    1587      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8587
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1943
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          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: 2476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2476
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 11, 'TRANS': 296}
          Chain breaks: 1
    Chain: "T"
      Number of atoms: 171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 171
          Classifications: {'peptide': 21}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 20}
  Time building chain proxies: 5.35, per 1000 atoms: 0.62
  Number of scatterers: 8587
  At special positions: 0
  Unit cell: (85.44, 103.68, 144.96, 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      67     16.00
     O    1587      8.00
     N    1484      7.00
     C    5449      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  69 " - pdb=" SG  CYS R 341 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 158 " - pdb=" SG  CYS R 239 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T   1 " - pdb=" SG  CYS T  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS T   3 " - pdb=" SG  CYS T  11 " 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: 2.15
  Conformation dependent library (CDL) restraints added in 945.3 milliseconds
  

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 12 sheets defined
      40.5% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 38
      removed outlier: 3.577A  pdb=" N   GLN A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 60
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.622A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 321 through 342
      removed outlier: 3.793A  pdb=" N   ARG A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   SER A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR A 340 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 379
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.950A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 45
      removed outlier: 3.722A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.701A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 61 through 65
      removed outlier: 3.676A  pdb=" N   LYS N  65 " --> pdb=" O   GLY N  62 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 108
      removed outlier: 4.045A  pdb=" N   ILE R  92 " --> pdb=" O   CYS R  88 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL R  93 " --> pdb=" O   THR R  89 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN R  98 " --> pdb=" O   GLY R  94 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ILE R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ILE R 105 " --> pdb=" O   LEU R 101 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TYR R 106 " --> pdb=" O   LEU R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 113 through 143
      removed outlier: 3.627A  pdb=" N   LEU R 118 " --> pdb=" O   GLY R 114 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      Proline residue:  R 135  - end of helix
    Processing helix  chain 'R' and resid 151 through 188
      removed outlier: 3.809A  pdb=" N   VAL R 155 " --> pdb=" O   ASN R 151 " (cutoff:3.500A)
      Proline residue:  R 162  - end of helix
      removed outlier: 3.627A  pdb=" N   TYR R 184 " --> pdb=" O   SER R 180 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG R 185 " --> pdb=" O   VAL R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 216
    Processing helix  chain 'R' and resid 217 through 222
    Processing helix  chain 'R' and resid 245 through 254
    Processing helix  chain 'R' and resid 255 through 284
      removed outlier: 3.977A  pdb=" N   TYR R 263 " --> pdb=" O   LEU R 259 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   MET R 266 " --> pdb=" O   PHE R 262 " (cutoff:3.500A)
      Proline residue:  R 267  - end of helix
      removed outlier: 3.854A  pdb=" N   TYR R 275 " --> pdb=" O   THR R 271 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLU R 281 " --> pdb=" O   LEU R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 332
      removed outlier: 4.101A  pdb=" N   LYS R 299 " --> pdb=" O   SER R 295 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   GLN R 300 " --> pdb=" O   GLU R 296 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU R 311 " --> pdb=" O   THR R 307 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL R 312 " --> pdb=" O   VAL R 308 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 339 through 360
      removed outlier: 3.696A  pdb=" N   LEU R 343 " --> pdb=" O   ASN R 339 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU R 349 " --> pdb=" O   SER R 345 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   MET R 350 " --> pdb=" O   PHE R 346 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASP R 351 " --> pdb=" O   LEU R 347 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   MET R 360 " --> pdb=" O   ASN R 356 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 363 through 371
      removed outlier: 3.840A  pdb=" N   LEU R 369 " --> pdb=" O   ASN R 365 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TYR R 370 " --> pdb=" O   PRO R 366 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE R 371 " --> pdb=" O   ILE R 367 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 375 through 382
      removed outlier: 3.636A  pdb=" N   CYS R 379 " --> pdb=" O   LYS R 375 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 8 through 17
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 5.939A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.172A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.194A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   HIS A 352 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU A 279 " --> pdb=" O   HIS A 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.985A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  49 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 3.595A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 3.870A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.573A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.519A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 189
      removed outlier: 6.894A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.978A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277
      removed outlier: 3.948A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 59
      removed outlier: 3.666A  pdb=" N   VAL N  48 " --> pdb=" O   TRP N  36 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 225 through 227
      removed outlier: 4.132A  pdb=" N   THR R 238 " --> pdb=" O   VAL R 227 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'R' and resid 230 through 231

    386 hydrogen bonds defined for protein.
    1125 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: 2.41

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2808
        1.34 -     1.47: 2110
        1.47 -     1.59: 3750
        1.59 -     1.71: 0
        1.71 -     1.83: 93
  Bond restraints: 8761
  Sorted by residual:
  bond pdb=" C   ARG N  98 "
       pdb=" N   CYS N  99 "
    ideal  model  delta    sigma   weight residual
    1.331  1.294  0.037 2.07e-02 2.33e+03 3.17e+00
  bond pdb=" CB  LYS A 216 "
       pdb=" CG  LYS A 216 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.44e+00
  bond pdb=" CG  LYS A 216 "
       pdb=" CD  LYS A 216 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" CA  ASP A 313 "
       pdb=" CB  ASP A 313 "
    ideal  model  delta    sigma   weight residual
    1.536  1.563 -0.028 2.53e-02 1.56e+03 1.19e+00
  bond pdb=" CB  ASP B 298 "
       pdb=" CG  ASP B 298 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.11e+00
  ... (remaining 8756 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 11682
        2.15 -     4.30: 147
        4.30 -     6.44: 19
        6.44 -     8.59: 3
        8.59 -    10.74: 3
  Bond angle restraints: 11854
  Sorted by residual:
  angle pdb=" CB  MET R 266 "
        pdb=" CG  MET R 266 "
        pdb=" SD  MET R 266 "
      ideal   model   delta    sigma   weight residual
     112.70  123.44  -10.74 3.00e+00 1.11e-01 1.28e+01
  angle pdb=" CB  LYS A 216 "
        pdb=" CG  LYS A 216 "
        pdb=" CD  LYS A 216 "
      ideal   model   delta    sigma   weight residual
     111.30  119.37   -8.07 2.30e+00 1.89e-01 1.23e+01
  angle pdb=" CA  GLN R  72 "
        pdb=" CB  GLN R  72 "
        pdb=" CG  GLN R  72 "
      ideal   model   delta    sigma   weight residual
     114.10  119.44   -5.34 2.00e+00 2.50e-01 7.12e+00
  angle pdb=" CA  LEU T  17 "
        pdb=" CB  LEU T  17 "
        pdb=" CG  LEU T  17 "
      ideal   model   delta    sigma   weight residual
     116.30  125.43   -9.13 3.50e+00 8.16e-02 6.81e+00
  angle pdb=" CA  LEU B 198 "
        pdb=" CB  LEU B 198 "
        pdb=" CG  LEU B 198 "
      ideal   model   delta    sigma   weight residual
     116.30  125.34   -9.04 3.50e+00 8.16e-02 6.68e+00
  ... (remaining 11849 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 4449
       17.48 -    34.97: 588
       34.97 -    52.45: 188
       52.45 -    69.93: 17
       69.93 -    87.42: 9
  Dihedral angle restraints: 5251
    sinusoidal: 2094
      harmonic: 3157
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    7.74   85.26     1      1.00e+01 1.00e-02 8.81e+01
  dihedral pdb=" CB  CYS R  69 "
           pdb=" SG  CYS R  69 "
           pdb=" SG  CYS R 341 "
           pdb=" CB  CYS R 341 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.92  -64.92     1      1.00e+01 1.00e-02 5.53e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.89   48.11     1      1.00e+01 1.00e-02 3.19e+01
  ... (remaining 5248 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 872
       0.035 -    0.070: 311
       0.070 -    0.105: 112
       0.105 -    0.140: 33
       0.140 -    0.175: 1
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CB  ILE B  43 "
            pdb=" CA  ILE B  43 "
            pdb=" CG1 ILE B  43 "
            pdb=" CG2 ILE B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" CG  LEU R 349 "
            pdb=" CB  LEU R 349 "
            pdb=" CD1 LEU R 349 "
            pdb=" CD2 LEU R 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE R  75 "
            pdb=" N   ILE R  75 "
            pdb=" C   ILE R  75 "
            pdb=" CB  ILE R  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 1513
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 227 "   -0.051 5.00e-02 4.00e+02   7.84e-02 9.83e+00
        pdb=" N   PRO R 228 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO R 228 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO R 228 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.02e+00
        pdb=" N   PRO B 236 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 304 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   GLU A 304 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A 304 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 305 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1510 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 823
        2.74 -     3.28: 8290
        3.28 -     3.82: 13814
        3.82 -     4.36: 15342
        4.36 -     4.90: 27009
  Nonbonded interactions: 65278
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   MET R 111 "
            pdb=" ND2 ASN R 116 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   TYR B  85 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OD1 ASP T  18 "
            pdb=" N   ILE T  19 "
     model   vdw
     2.238 3.120
  ... (remaining 65273 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.620
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
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      :  0.004   0.037   8761  Z= 0.234
  Angle     :  0.621  10.740  11854  Z= 0.328
  Chirality :  0.043   0.175   1329
  Planarity :  0.004   0.078   1513
  Dihedral  : 16.873  87.416   3189
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 33.33 %
    Favored  : 66.24 %
  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: -0.52 (0.26), residues: 1068
  helix:  1.23 (0.27), residues: 408
  sheet: -0.28 (0.39), residues: 197
  loop : -1.87 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.022   0.002   PHE B 151 
 TYR   0.019   0.002   TYR A 253 
 ARG   0.010   0.000   ARG B  68 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 213
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7307 (mtmm)
REVERT: R  137 ASN cc_start: 0.7780 (m-40) cc_final: 0.7374 (m110)
  outliers start: 4
  outliers final: 3
  residues processed: 215
  average time/residue: 0.2784
  time to fit residues: 77.6826
Evaluate side-chains
  214 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 211
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  237 LYS
Chi-restraints excluded: chain R residue  361 ASN
Chi-restraints excluded: chain R residue  367 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.0770
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 356 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.167875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.140058 restraints weight = 12753.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.74
r_work: 0.3635 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.0697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8761  Z= 0.198
  Angle     :  0.556  11.023  11854  Z= 0.293
  Chirality :  0.041   0.158   1329
  Planarity :  0.004   0.055   1513
  Dihedral  :  4.990  44.971   1185
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 28.97 %
    Favored  : 66.77 %
  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: -0.15 (0.26), residues: 1068
  helix:  1.60 (0.26), residues: 421
  sheet: -0.17 (0.38), residues: 206
  loop : -1.81 (0.27), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.020   0.001   PHE N 108 
 TYR   0.016   0.001   TYR A 253 
 ARG   0.007   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 211
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.7394 (m-30) cc_final: 0.7114 (m-30)
REVERT: N   36 TRP cc_start: 0.7977 (m100) cc_final: 0.7353 (m100)
REVERT: R   79 PHE cc_start: 0.7459 (t80) cc_final: 0.7217 (t80)
REVERT: R   83 ASN cc_start: 0.6269 (OUTLIER) cc_final: 0.6007 (m-40)
REVERT: R  196 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6839 (tt)
  outliers start: 40
  outliers final: 21
  residues processed: 234
  average time/residue: 0.2461
  time to fit residues: 75.7999
Evaluate side-chains
  229 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  379 ARG
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   83 ASN
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  355 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 137 ASN
R 323 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.167143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.138769 restraints weight = 12866.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.80
r_work: 0.3611 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.0876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8761  Z= 0.269
  Angle     :  0.575   8.797  11854  Z= 0.304
  Chirality :  0.043   0.187   1329
  Planarity :  0.004   0.047   1513
  Dihedral  :  4.540  21.224   1177
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 27.90 %
    Favored  : 67.52 %
  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: -0.20 (0.26), residues: 1068
  helix:  1.61 (0.26), residues: 421
  sheet: -0.24 (0.39), residues: 203
  loop : -1.85 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.025   0.002   PHE N 108 
 TYR   0.013   0.002   TYR A 253 
 ARG   0.007   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 211
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7677 (ptm160)
REVERT: A  333 ASP cc_start: 0.7058 (m-30) cc_final: 0.6738 (m-30)
REVERT: B  228 ASP cc_start: 0.7441 (m-30) cc_final: 0.7064 (m-30)
REVERT: B  246 ASP cc_start: 0.7423 (t70) cc_final: 0.7159 (t0)
REVERT: N   36 TRP cc_start: 0.8112 (m100) cc_final: 0.7423 (m100)
REVERT: R   91 PHE cc_start: 0.7796 (t80) cc_final: 0.7553 (t80)
REVERT: R  111 MET cc_start: 0.5900 (tpt) cc_final: 0.5568 (tpt)
REVERT: R  113 ASN cc_start: 0.6273 (p0) cc_final: 0.5944 (p0)
REVERT: R  196 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6856 (tt)
REVERT: T    7 MET cc_start: 0.7822 (pmm) cc_final: 0.7410 (pmm)
  outliers start: 43
  outliers final: 32
  residues processed: 236
  average time/residue: 0.2502
  time to fit residues: 77.4770
Evaluate side-chains
  243 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  314 ILE
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 93 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.169194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.141331 restraints weight = 12726.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.71
r_work: 0.3645 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.1120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8761  Z= 0.167
  Angle     :  0.535   8.537  11854  Z= 0.279
  Chirality :  0.041   0.200   1329
  Planarity :  0.003   0.049   1513
  Dihedral  :  4.281  20.227   1177
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 28.01 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.26), residues: 1068
  helix:  1.71 (0.26), residues: 422
  sheet: -0.30 (0.38), residues: 209
  loop : -1.75 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.017   0.001   PHE N 108 
 TYR   0.010   0.001   TYR A 253 
 ARG   0.002   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 210
  time to evaluate  : 0.876 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7634 (ptm160)
REVERT: A  377 ASN cc_start: 0.7807 (m-40) cc_final: 0.7536 (m-40)
REVERT: B  228 ASP cc_start: 0.7438 (m-30) cc_final: 0.7002 (m-30)
REVERT: B  246 ASP cc_start: 0.7447 (t70) cc_final: 0.7062 (t0)
REVERT: N   36 TRP cc_start: 0.7969 (m100) cc_final: 0.7344 (m100)
REVERT: N   60 TYR cc_start: 0.7844 (m-80) cc_final: 0.7185 (m-80)
REVERT: R   72 GLN cc_start: 0.7201 (pp30) cc_final: 0.6967 (pp30)
REVERT: R   91 PHE cc_start: 0.7848 (t80) cc_final: 0.7635 (t80)
REVERT: R  133 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5381 (m-30)
REVERT: R  196 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6838 (tt)
REVERT: R  215 ILE cc_start: 0.7605 (tt) cc_final: 0.7360 (tt)
REVERT: R  360 MET cc_start: 0.7862 (mmm) cc_final: 0.7635 (tpp)
REVERT: T    7 MET cc_start: 0.7832 (pmm) cc_final: 0.7516 (pmm)
  outliers start: 47
  outliers final: 32
  residues processed: 238
  average time/residue: 0.2550
  time to fit residues: 79.8711
Evaluate side-chains
  240 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  196 ILE
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 86 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 33 optimal weight:    0.4980
   chunk 68 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
R 137 ASN
** R 175 ASN ** 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 = 0.4137 r_free = 0.4137 target = 0.168496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.140343 restraints weight = 12729.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.76
r_work: 0.3652 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6878
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8761  Z= 0.166
  Angle     :  0.539   8.490  11854  Z= 0.278
  Chirality :  0.041   0.202   1329
  Planarity :  0.003   0.050   1513
  Dihedral  :  4.175  19.619   1177
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 28.12 %
    Favored  : 66.88 %
  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:  0.00 (0.26), residues: 1068
  helix:  1.80 (0.26), residues: 419
  sheet: -0.14 (0.39), residues: 202
  loop : -1.74 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.016   0.001   PHE N 108 
 TYR   0.009   0.001   TYR A 253 
 ARG   0.003   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 210
  time to evaluate  : 0.878 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7666 (ptm160)
REVERT: A  377 ASN cc_start: 0.7765 (m-40) cc_final: 0.7513 (m-40)
REVERT: B   47 THR cc_start: 0.8614 (t) cc_final: 0.7873 (p)
REVERT: B  246 ASP cc_start: 0.7512 (t70) cc_final: 0.7239 (t0)
REVERT: N   36 TRP cc_start: 0.7997 (m100) cc_final: 0.7351 (m100)
REVERT: N   60 TYR cc_start: 0.7889 (m-80) cc_final: 0.7222 (m-80)
REVERT: R   72 GLN cc_start: 0.7217 (pp30) cc_final: 0.6972 (pp30)
REVERT: R   91 PHE cc_start: 0.7857 (t80) cc_final: 0.7646 (t80)
REVERT: R  133 ASP cc_start: 0.5807 (OUTLIER) cc_final: 0.5596 (m-30)
REVERT: R  137 ASN cc_start: 0.7773 (m-40) cc_final: 0.7292 (m110)
REVERT: R  174 LEU cc_start: 0.8125 (mt) cc_final: 0.7923 (mm)
REVERT: R  196 ILE cc_start: 0.7008 (tt) cc_final: 0.6793 (tt)
REVERT: R  215 ILE cc_start: 0.7619 (tt) cc_final: 0.7364 (tt)
REVERT: R  360 MET cc_start: 0.7796 (mmm) cc_final: 0.7593 (tpp)
  outliers start: 47
  outliers final: 36
  residues processed: 240
  average time/residue: 0.2519
  time to fit residues: 79.9330
Evaluate side-chains
  247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 209
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LYS
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 297 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.167744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139574 restraints weight = 12640.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.76
r_work: 0.3624 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8761  Z= 0.239
  Angle     :  0.570   8.781  11854  Z= 0.297
  Chirality :  0.042   0.194   1329
  Planarity :  0.004   0.051   1513
  Dihedral  :  4.331  20.283   1177
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 27.58 %
    Favored  : 66.77 %
  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:  0.00 (0.27), residues: 1068
  helix:  1.78 (0.26), residues: 419
  sheet: -0.15 (0.38), residues: 209
  loop : -1.75 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.022   0.002   PHE N 108 
 TYR   0.011   0.001   TYR A 329 
 ARG   0.008   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 212
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A  255 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7677 (ptm160)
REVERT: B   59 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7644 (m-80)
REVERT: B   68 ARG cc_start: 0.7144 (ttt-90) cc_final: 0.6835 (ttt-90)
REVERT: B  228 ASP cc_start: 0.7374 (m-30) cc_final: 0.6999 (m-30)
REVERT: B  246 ASP cc_start: 0.7451 (t70) cc_final: 0.6964 (t70)
REVERT: B  322 ASP cc_start: 0.7134 (m-30) cc_final: 0.6886 (m-30)
REVERT: N   36 TRP cc_start: 0.8115 (m100) cc_final: 0.7434 (m100)
REVERT: N   60 TYR cc_start: 0.7929 (m-80) cc_final: 0.7264 (m-80)
REVERT: R   95 MET cc_start: 0.7044 (mmm) cc_final: 0.6795 (mmm)
REVERT: R  111 MET cc_start: 0.5885 (tpt) cc_final: 0.5394 (tpt)
REVERT: R  113 ASN cc_start: 0.6143 (p0) cc_final: 0.5677 (p0)
REVERT: R  133 ASP cc_start: 0.5793 (OUTLIER) cc_final: 0.5414 (m-30)
REVERT: R  174 LEU cc_start: 0.8141 (mt) cc_final: 0.7809 (mp)
REVERT: R  215 ILE cc_start: 0.7667 (tt) cc_final: 0.7406 (tt)
REVERT: R  360 MET cc_start: 0.7932 (mmm) cc_final: 0.7718 (mmm)
REVERT: T   18 ASP cc_start: 0.8171 (t0) cc_final: 0.7958 (t0)
  outliers start: 53
  outliers final: 42
  residues processed: 245
  average time/residue: 0.2366
  time to fit residues: 76.2998
Evaluate side-chains
  253 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 208
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue   73 THR
Chi-restraints excluded: chain R residue   93 VAL
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  172 THR
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  309 PHE
Chi-restraints excluded: chain R residue  347 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Chi-restraints excluded: chain T residue   20 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 71 optimal weight:    0.5980
   chunk 102 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 44 optimal weight:    0.1980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 137 ASN
R 175 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.170256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.141990 restraints weight = 12795.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.79
r_work: 0.3658 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.1461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8761  Z= 0.152
  Angle     :  0.540   9.078  11854  Z= 0.276
  Chirality :  0.041   0.214   1329
  Planarity :  0.003   0.051   1513
  Dihedral  :  4.129  19.088   1177
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 28.22 %
    Favored  : 66.24 %
  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:  0.11 (0.27), residues: 1068
  helix:  1.83 (0.26), residues: 421
  sheet: -0.14 (0.39), residues: 207
  loop : -1.62 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.013   0.001   PHE N 108 
 TYR   0.008   0.001   TYR A 253 
 ARG   0.008   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 209
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.7307 (mtpt) cc_final: 0.7036 (mtmm)
REVERT: A  255 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7673 (ptm160)
REVERT: B   47 THR cc_start: 0.8597 (t) cc_final: 0.7824 (p)
REVERT: B   59 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7566 (m-80)
REVERT: B  126 LEU cc_start: 0.8332 (mm) cc_final: 0.8064 (mm)
REVERT: B  228 ASP cc_start: 0.7344 (m-30) cc_final: 0.6884 (m-30)
REVERT: B  246 ASP cc_start: 0.7483 (t70) cc_final: 0.6955 (t70)
REVERT: N   36 TRP cc_start: 0.7985 (m100) cc_final: 0.7325 (m100)
REVERT: R   95 MET cc_start: 0.7038 (mmm) cc_final: 0.6774 (mmm)
REVERT: R   98 ASN cc_start: 0.7353 (m-40) cc_final: 0.7011 (t0)
REVERT: R  133 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5550 (m-30)
REVERT: R  137 ASN cc_start: 0.7716 (m-40) cc_final: 0.7272 (m110)
REVERT: R  309 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6696 (t80)
REVERT: T    7 MET cc_start: 0.7797 (pmm) cc_final: 0.7563 (pmm)
  outliers start: 52
  outliers final: 40
  residues processed: 243
  average time/residue: 0.2351
  time to fit residues: 75.3266
Evaluate side-chains
  249 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 205
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  133 ASP
Chi-restraints excluded: chain R residue  175 ASN
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  198 ILE
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  309 PHE
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Chi-restraints excluded: chain T residue   20 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 99 optimal weight:    0.0010
   chunk 101 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.3382

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

Flipped N/Q/H residues before XYZ refinement:
R 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.170940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.142464 restraints weight = 12955.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.84
r_work: 0.3664 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8761  Z= 0.151
  Angle     :  0.556   9.145  11854  Z= 0.282
  Chirality :  0.042   0.258   1329
  Planarity :  0.003   0.051   1513
  Dihedral  :  4.033  18.651   1177
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 29.39 %
    Favored  : 65.92 %
  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:  0.10 (0.27), residues: 1068
  helix:  1.79 (0.26), residues: 421
  sheet: -0.02 (0.39), residues: 202
  loop : -1.63 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 352 
 PHE   0.012   0.001   PHE N 108 
 TYR   0.008   0.001   TYR A 253 
 ARG   0.008   0.000   ARG N  98 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 211
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.7270 (mtpt) cc_final: 0.7008 (mtmm)
REVERT: A  255 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7683 (ptm160)
REVERT: B   47 THR cc_start: 0.8602 (t) cc_final: 0.7793 (p)
REVERT: B   59 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7567 (m-80)
REVERT: B  126 LEU cc_start: 0.8318 (mm) cc_final: 0.8059 (mm)
REVERT: B  228 ASP cc_start: 0.7359 (m-30) cc_final: 0.6899 (m-30)
REVERT: B  246 ASP cc_start: 0.7480 (t70) cc_final: 0.6964 (t70)
REVERT: N   36 TRP cc_start: 0.7949 (m100) cc_final: 0.7306 (m100)
REVERT: R   95 MET cc_start: 0.7057 (mmm) cc_final: 0.6773 (mmm)
REVERT: R  137 ASN cc_start: 0.7733 (m-40) cc_final: 0.7270 (m110)
REVERT: R  309 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6672 (t80)
REVERT: T    7 MET cc_start: 0.7792 (pmm) cc_final: 0.7581 (pmm)
  outliers start: 44
  outliers final: 37
  residues processed: 240
  average time/residue: 0.2436
  time to fit residues: 77.0471
Evaluate side-chains
  248 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 208
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  175 ASN
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  309 PHE
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Chi-restraints excluded: chain T residue   20 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 175 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.169748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141668 restraints weight = 12769.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.72
r_work: 0.3653 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8761  Z= 0.194
  Angle     :  0.578  10.118  11854  Z= 0.293
  Chirality :  0.042   0.251   1329
  Planarity :  0.003   0.051   1513
  Dihedral  :  4.110  19.272   1177
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 29.93 %
    Favored  : 66.03 %
  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:  0.10 (0.27), residues: 1068
  helix:  1.80 (0.26), residues: 421
  sheet: -0.08 (0.39), residues: 204
  loop : -1.64 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 352 
 PHE   0.019   0.001   PHE N 108 
 TYR   0.010   0.001   TYR A 329 
 ARG   0.004   0.000   ARG B 137 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 209
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.7293 (mtpt) cc_final: 0.7033 (mtmm)
REVERT: A  255 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (ptm160)
REVERT: B   47 THR cc_start: 0.8641 (t) cc_final: 0.7855 (p)
REVERT: B   59 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7510 (m-80)
REVERT: B  126 LEU cc_start: 0.8329 (mm) cc_final: 0.8043 (mm)
REVERT: B  228 ASP cc_start: 0.7351 (m-30) cc_final: 0.6919 (m-30)
REVERT: B  246 ASP cc_start: 0.7470 (t70) cc_final: 0.6992 (t70)
REVERT: N   36 TRP cc_start: 0.8009 (m100) cc_final: 0.7375 (m100)
REVERT: R   95 MET cc_start: 0.7002 (mmm) cc_final: 0.6731 (mmm)
REVERT: R  137 ASN cc_start: 0.7736 (m-40) cc_final: 0.7268 (m110)
REVERT: R  215 ILE cc_start: 0.7580 (tt) cc_final: 0.7338 (tt)
  outliers start: 38
  outliers final: 34
  residues processed: 234
  average time/residue: 0.2489
  time to fit residues: 75.7944
Evaluate side-chains
  244 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 208
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  175 ASN
Chi-restraints excluded: chain R residue  176 LEU
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  309 PHE
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 97 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 175 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.167732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139686 restraints weight = 12777.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.73
r_work: 0.3624 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8761  Z= 0.263
  Angle     :  0.625  10.437  11854  Z= 0.318
  Chirality :  0.044   0.234   1329
  Planarity :  0.004   0.051   1513
  Dihedral  :  4.367  20.201   1177
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 30.24 %
    Favored  : 65.92 %
  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:  0.03 (0.27), residues: 1068
  helix:  1.73 (0.26), residues: 418
  sheet: -0.01 (0.39), residues: 202
  loop : -1.68 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 220 
 PHE   0.026   0.002   PHE N 108 
 TYR   0.012   0.002   TYR N  60 
 ARG   0.005   0.000   ARG B 137 

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

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

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2136 Ramachandran restraints generated.
    1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 209
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  333 ASP cc_start: 0.7056 (m-30) cc_final: 0.6802 (m-30)
REVERT: B   59 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7532 (m-80)
REVERT: B   68 ARG cc_start: 0.7203 (ttt-90) cc_final: 0.6968 (ttt-90)
REVERT: B   78 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7226 (mptt)
REVERT: B  228 ASP cc_start: 0.7502 (m-30) cc_final: 0.7232 (m-30)
REVERT: B  246 ASP cc_start: 0.7422 (t70) cc_final: 0.7073 (t0)
REVERT: N   36 TRP cc_start: 0.8136 (m100) cc_final: 0.7494 (m100)
REVERT: N   60 TYR cc_start: 0.7921 (m-80) cc_final: 0.7274 (m-80)
REVERT: R   95 MET cc_start: 0.7019 (mmm) cc_final: 0.6752 (mmm)
REVERT: R  111 MET cc_start: 0.5382 (tpt) cc_final: 0.4595 (tpt)
REVERT: R  113 ASN cc_start: 0.6144 (p0) cc_final: 0.5732 (p0)
REVERT: R  137 ASN cc_start: 0.7742 (m-40) cc_final: 0.7331 (m110)
REVERT: R  215 ILE cc_start: 0.7651 (tt) cc_final: 0.7404 (tt)
REVERT: T   18 ASP cc_start: 0.8025 (t0) cc_final: 0.7788 (t0)
  outliers start: 36
  outliers final: 33
  residues processed: 233
  average time/residue: 0.2401
  time to fit residues: 73.7246
Evaluate side-chains
  243 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  276 SER
Chi-restraints excluded: chain A residue  310 THR
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  103 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  290 ASP
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   51 ILE
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain R residue  175 ASN
Chi-restraints excluded: chain R residue  270 CYS
Chi-restraints excluded: chain R residue  309 PHE
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  367 ILE
Chi-restraints excluded: chain T residue   17 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 101 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
R  83 ASN
** R 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 175 ASN ** 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 = 0.4088 r_free = 0.4088 target = 0.164219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.136300 restraints weight = 12807.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.71
r_work: 0.3596 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8761  Z= 0.389
  Angle     :  0.703  11.143  11854  Z= 0.364
  Chirality :  0.047   0.230   1329
  Planarity :  0.004   0.052   1513
  Dihedral  :  4.845  21.372   1177
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 30.56 %
    Favored  : 65.39 %
  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: -0.27 (0.26), residues: 1068
  helix:  1.51 (0.26), residues: 415
  sheet: -0.18 (0.39), residues: 196
  loop : -1.82 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R 146 
 HIS   0.007   0.002   HIS A 220 
 PHE   0.033   0.002   PHE N 108 
 TYR   0.021   0.002   TYR R 263 
 ARG   0.006   0.000   ARG B 137 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4746.16 seconds
wall clock time: 83 minutes 46.47 seconds (5026.47 seconds total)