Starting phenix.real_space_refine
on Sun Oct 25 10:01:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/24gt_69496/10_2026/24gt_69496.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.009
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      49      5.16       5
     C   10055      2.51       5
     N    2790      2.21       5
     O    3157      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16051
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 788, 6233
          Classifications: {'peptide': 788}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 758}
    Chain: "B"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2795
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
    Chain: "C"
      Number of atoms: 1414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1414
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
    Chain: "D"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1761
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 700
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 5, 'TRANS': 84}
    Chain: "F"
      Number of atoms: 3148
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3148
          Classifications: {'peptide': 406}
          Link IDs: {'PTRANS': 13, 'TRANS': 392}
  Time building chain proxies: 2.96, per 1000 atoms: 0.18
  Number of scatterers: 16051
  At special positions: 0
  Unit cell: (127.84, 118.064, 147.392, 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      49     16.00
     O    3157      8.00
     N    2790      7.00
     C   10055      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  57 " - pdb=" SG  CYS F 297 " 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: 1.22
  Conformation dependent library (CDL) restraints added in 682.8 milliseconds
  

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3786

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 22 sheets defined
      32.8% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 3.669A  pdb=" N   ILE A  59 " --> pdb=" O   ASN A  55 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLY A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
    Processing helix  chain 'A' and resid 126 through 144
    Processing helix  chain 'A' and resid 189 through 196
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.729A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 393
      removed outlier: 3.825A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
      removed outlier: 4.712A  pdb=" N   ASN A 731 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 377
      removed outlier: 4.261A  pdb=" N   GLY B 376 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 39 through 43
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 112 through 114
      No H-bonds generated for 'chain 'C' and resid 112 through 114'
    Processing helix  chain 'C' and resid 115 through 127
    Processing helix  chain 'C' and resid 190 through 214
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 61
    Processing helix  chain 'D' and resid 68 through 83
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 120
      removed outlier: 3.511A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP D 120 " --> pdb=" O   ASN D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 128
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.554A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 229 through 243
      removed outlier: 3.640A  pdb=" N   SER D 243 " --> pdb=" O   ALA D 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 27
    Processing helix  chain 'E' and resid 39 through 46
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 38 through 57
    Processing helix  chain 'F' and resid 62 through 88
    Processing helix  chain 'F' and resid 92 through 107
    Processing helix  chain 'F' and resid 110 through 121
    Processing helix  chain 'F' and resid 124 through 150
    Processing helix  chain 'F' and resid 153 through 167
    Processing helix  chain 'F' and resid 188 through 208
    Processing helix  chain 'F' and resid 211 through 219
    Processing helix  chain 'F' and resid 222 through 228
    Processing helix  chain 'F' and resid 240 through 249
    Processing helix  chain 'F' and resid 299 through 316
    Processing helix  chain 'F' and resid 320 through 329
    Processing helix  chain 'F' and resid 333 through 338
    Processing helix  chain 'F' and resid 345 through 349
    Processing helix  chain 'F' and resid 350 through 360
    Processing helix  chain 'F' and resid 388 through 420
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 5.966A  pdb=" N   VAL A 163 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 7.894A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.465A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ILE A 182 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ILE A 260 " --> pdb=" O   ILE A 182 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 273
      removed outlier: 6.966A  pdb=" N   LEU A 337 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL A 339 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.477A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 430
      removed outlier: 3.892A  pdb=" N   LYS A 507 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 791 " --> pdb=" O   MET A 768 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.923A  pdb=" N   ASP A 704 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   SER A 702 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 51
      removed outlier: 7.171A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER B  49 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL B 387 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68
      removed outlier: 6.591A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 111 through 118
      removed outlier: 4.643A  pdb=" N   GLY B 114 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLY B 125 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN B 130 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   VAL B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   GLN B 144 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   ALA B 133 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 6.389A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 206 through 210
      removed outlier: 6.828A  pdb=" N   VAL B 216 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   GLN B 229 " --> pdb=" O   VAL B 216 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA B 218 " --> pdb=" O   ILE B 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 6.974A  pdb=" N   LEU B 267 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   LYS B 280 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA B 269 " --> pdb=" O   MET B 278 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 5.703A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 96 through 100
    Processing sheet with id=AB8, first strand: chain 'C' and resid 131 through 135
      removed outlier: 6.322A  pdb=" N   THR C 142 " --> pdb=" O   THR C 132 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ARG C 134 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   THR C 140 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   THR C 140 " --> pdb=" O   VAL C 165 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL C 165 " --> pdb=" O   THR C 140 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   THR C 142 " --> pdb=" O   ILE C 163 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ILE C 163 " --> pdb=" O   THR C 142 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   ASP C 144 " --> pdb=" O   TYR C 161 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR C 161 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   TYR C 157 " --> pdb=" O   TRP C 148 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN C 180 " --> pdb=" O   ARG C 160 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   GLN C 162 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   LEU C 178 " --> pdb=" O   GLN C 162 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   SER C 164 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   VAL C 176 " --> pdb=" O   SER C 164 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LYS C 166 " --> pdb=" O   VAL C 174 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   VAL C 174 " --> pdb=" O   LYS C 166 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.667A  pdb=" N   ILE E  32 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.667A  pdb=" N   ILE E  32 " --> pdb=" O   GLN E  80 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 37
    Processing sheet with id=AC3, first strand: chain 'F' and resid 232 through 235
      removed outlier: 3.565A  pdb=" N   ASP F 272 " --> pdb=" O   ASN F 175 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   SER F 177 " --> pdb=" O   VAL F 270 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   VAL F 270 " --> pdb=" O   SER F 177 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   ILE F 179 " --> pdb=" O   LEU F 268 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   LEU F 268 " --> pdb=" O   ILE F 179 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ILE F 181 " --> pdb=" O   HIS F 266 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   HIS F 266 " --> pdb=" O   ILE F 181 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 340 through 344
      removed outlier: 5.189A  pdb=" N   ASP F 340 " --> pdb=" O   HIS F 289 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   HIS F 289 " --> pdb=" O   ASP F 340 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLY F 342 " --> pdb=" O   ALA F 287 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ALA F 287 " --> pdb=" O   GLY F 342 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ARG F 288 " --> pdb=" O   LEU F 380 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   LEU F 380 " --> pdb=" O   ARG F 288 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ILE F 290 " --> pdb=" O   ILE F 378 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   ILE F 378 " --> pdb=" O   ILE F 290 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   LEU F 292 " --> pdb=" O   HIS F 376 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   HIS F 376 " --> pdb=" O   LEU F 292 " (cutoff:3.500A)

    799 hydrogen bonds defined for protein.
    2223 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: 3.01

  Time building geometry restraints manager: 1.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4999
        1.33 -     1.46: 3246
        1.46 -     1.58: 8027
        1.58 -     1.71: 0
        1.71 -     1.83: 96
  Bond restraints: 16368
  Sorted by residual:
  bond pdb=" CB  VAL A  54 "
       pdb=" CG2 VAL A  54 "
    ideal  model  delta    sigma   weight residual
    1.521  1.405  0.116 3.30e-02 9.18e+02 1.23e+01
  bond pdb=" N   ILE A 430 "
       pdb=" CA  ILE A 430 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.14e-02 7.69e+03 1.19e+01
  bond pdb=" N   THR A  53 "
       pdb=" CA  THR A  53 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.044 1.29e-02 6.01e+03 1.15e+01
  bond pdb=" N   VAL B  30 "
       pdb=" CA  VAL B  30 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" N   VAL A  26 "
       pdb=" CA  VAL A  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.19e-02 7.06e+03 1.03e+01
  ... (remaining 16363 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.63: 21825
        3.63 -     7.25: 356
        7.25 -    10.88: 33
       10.88 -    14.51: 6
       14.51 -    18.13: 2
  Bond angle restraints: 22222
  Sorted by residual:
  angle pdb=" N   GLY A 424 "
        pdb=" CA  GLY A 424 "
        pdb=" C   GLY A 424 "
      ideal   model   delta    sigma   weight residual
     111.03  126.13  -15.10 1.40e+00 5.10e-01 1.16e+02
  angle pdb=" N   ILE F 181 "
        pdb=" CA  ILE F 181 "
        pdb=" C   ILE F 181 "
      ideal   model   delta    sigma   weight residual
     107.56  115.65   -8.09 9.10e-01 1.21e+00 7.91e+01
  angle pdb=" CG1 VAL A  54 "
        pdb=" CB  VAL A  54 "
        pdb=" CG2 VAL A  54 "
      ideal   model   delta    sigma   weight residual
     110.80   92.67   18.13 2.20e+00 2.07e-01 6.79e+01
  angle pdb=" N   GLY A 275 "
        pdb=" CA  GLY A 275 "
        pdb=" C   GLY A 275 "
      ideal   model   delta    sigma   weight residual
     113.99  124.52  -10.53 1.28e+00 6.10e-01 6.77e+01
  angle pdb=" CA  GLY B 114 "
        pdb=" C   GLY B 114 "
        pdb=" O   GLY B 114 "
      ideal   model   delta    sigma   weight residual
     122.45  117.48    4.97 7.20e-01 1.93e+00 4.77e+01
  ... (remaining 22217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 9108
       17.52 -    35.05: 528
       35.05 -    52.57: 81
       52.57 -    70.10: 53
       70.10 -    87.62: 11
  Dihedral angle restraints: 9781
    sinusoidal: 3855
      harmonic: 5926
  Sorted by residual:
  dihedral pdb=" CA  ASN B 266 "
           pdb=" C   ASN B 266 "
           pdb=" N   LEU B 267 "
           pdb=" CA  LEU B 267 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.28   25.72     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  SER F 366 "
           pdb=" C   SER F 366 "
           pdb=" N   ALA F 367 "
           pdb=" CA  ALA F 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.16   23.84     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  LYS A 808 "
           pdb=" C   LYS A 808 "
           pdb=" N   THR A 809 "
           pdb=" CA  THR A 809 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 9778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1869
       0.065 -    0.130: 480
       0.130 -    0.195: 72
       0.195 -    0.260: 22
       0.260 -    0.325: 3
  Chirality restraints: 2446
  Sorted by residual:
  chirality pdb=" CA  GLN F 113 "
            pdb=" N   GLN F 113 "
            pdb=" C   GLN F 113 "
            pdb=" CB  GLN F 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CA  MET F 231 "
            pdb=" N   MET F 231 "
            pdb=" C   MET F 231 "
            pdb=" CB  MET F 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CG  LEU A 125 "
            pdb=" CB  LEU A 125 "
            pdb=" CD1 LEU A 125 "
            pdb=" CD2 LEU A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 2443 not shown)

  Planarity restraints: 2940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 158 "   -0.022 2.00e-02 2.50e+03   4.41e-02 1.94e+01
        pdb=" C   LEU A 158 "    0.076 2.00e-02 2.50e+03
        pdb=" O   LEU A 158 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PRO A 159 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 546 "   -0.004 2.00e-02 2.50e+03   2.51e-02 1.58e+01
        pdb=" CG  TRP A 546 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 546 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 546 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 546 "    0.024 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 546 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 546 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 546 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 546 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 546 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E  69 "   -0.017 2.00e-02 2.50e+03   3.38e-02 1.14e+01
        pdb=" C   GLY E  69 "    0.058 2.00e-02 2.50e+03
        pdb=" O   GLY E  69 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   THR E  70 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2937 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 4523
        2.82 -     3.34: 16299
        3.34 -     3.86: 28315
        3.86 -     4.38: 32404
        4.38 -     4.90: 52752
  Nonbonded interactions: 134293
  Sorted by model distance:
  nonbonded pdb=" O   SER B 158 "
            pdb=" OD1 ASP B 159 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   GLY A 136 "
            pdb=" OD1 ASP A 139 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" O   LEU D  58 "
            pdb=" O   ARG D  61 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" O   GLN F 245 "
            pdb=" OG  SER F 248 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" OE1 GLU A 123 "
            pdb=" O   SER A 124 "
     model   vdw
     2.418 3.040
  ... (remaining 134288 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.230
  Find NCS groups from input model:        0.080
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.116  16369  Z= 0.363
  Angle     :  1.175  18.131  22224  Z= 0.729
  Chirality :  0.060   0.325   2446
  Planarity :  0.008   0.134   2940
  Dihedral  : 12.763  87.621   5992
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.47 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.39 %
    Favored  : 98.37 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.18), residues: 2047
  helix:  1.38 (0.19), residues: 613
  sheet:  0.70 (0.21), residues: 549
  loop : -0.17 (0.21), residues: 885

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG A 583 
 TYR   0.046   0.003   TYR A 548 
 PHE   0.034   0.003   PHE A 517 
 TRP   0.057   0.004   TRP A 546 
 HIS   0.010   0.002   HIS A 677 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00610 /  0.36 (16368)
  covalent geometry    : angle       1.17490 /  0.73 (22222)
  SS BOND              : bond        0.00190 /  0.12 (    1)
  SS BOND              : angle       0.85722 /  0.31 (    2)
  hydrogen bonds       : bond        0.12002 /  8.00 (  796)
  hydrogen bonds       : angle       6.69060 /  4.74 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 158
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 HIS cc_start: 0.9664 (m170) cc_final: 0.9456 (m-70)
REVERT: A  303 LYS cc_start: 0.9502 (ptpt) cc_final: 0.9259 (ptpp)
REVERT: A  304 MET cc_start: 0.9638 (mmp) cc_final: 0.9426 (mmm)
REVERT: B  165 HIS cc_start: 0.8783 (t70) cc_final: 0.8493 (t70)
REVERT: B  261 LEU cc_start: 0.9824 (tp) cc_final: 0.9606 (tp)
REVERT: B  263 TYR cc_start: 0.9477 (t80) cc_final: 0.9058 (t80)
REVERT: B  346 LEU cc_start: 0.9600 (tp) cc_final: 0.9319 (tp)
REVERT: C   99 PHE cc_start: 0.8646 (p90) cc_final: 0.8419 (p90)
REVERT: C  128 ASN cc_start: 0.9266 (m110) cc_final: 0.9014 (m-40)
REVERT: C  157 TYR cc_start: 0.9491 (m-80) cc_final: 0.9181 (m-80)
REVERT: C  186 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8992 (mppt)
REVERT: C  203 ASN cc_start: 0.9534 (p0) cc_final: 0.9012 (p0)
REVERT: D   74 ASP cc_start: 0.9247 (m-30) cc_final: 0.8880 (m-30)
REVERT: D  105 ILE cc_start: 0.9715 (pt) cc_final: 0.9440 (mm)
REVERT: D  225 MET cc_start: 0.9133 (mmm) cc_final: 0.8892 (mmm)
REVERT: E   64 MET cc_start: 0.9358 (mtp) cc_final: 0.9156 (mmm)
REVERT: E   93 LEU cc_start: 0.9778 (mt) cc_final: 0.9556 (mp)
REVERT: E  105 ASP cc_start: 0.9134 (t0) cc_final: 0.8819 (t0)
REVERT: F   71 MET cc_start: 0.9312 (ptt) cc_final: 0.8967 (ptt)
REVERT: F  114 MET cc_start: 0.9299 (mmp) cc_final: 0.9072 (mmm)
REVERT: F  128 TYR cc_start: 0.9476 (t80) cc_final: 0.9114 (t80)
REVERT: F  223 GLN cc_start: 0.8827 (mp10) cc_final: 0.8407 (pp30)
REVERT: F  413 TRP cc_start: 0.9175 (t-100) cc_final: 0.8918 (t60)
  outliers start: 4
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1310
  time to fit residues: 32.0338
Evaluate side-chains
  120 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122]
   chunk 98 optimal weight:    7.9990
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0070
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   30.0000
   overall best weight:    3.6006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 542 GLN
A 625 HIS
B  41 GLN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 ASN
** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 104 ASN
** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.054139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.035720 restraints weight = 125580.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.036950 restraints weight = 70845.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.037797 restraints weight = 49170.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.038354 restraints weight = 38750.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.038716 restraints weight = 33314.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  16369  Z= 0.182
  Angle     :  0.632   8.600  22224  Z= 0.338
  Chirality :  0.044   0.244   2446
  Planarity :  0.004   0.041   2940
  Dihedral  :  4.691  36.312   2247
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.34 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.72 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.18), residues: 2047
  helix:  1.72 (0.20), residues: 620
  sheet:  0.44 (0.20), residues: 594
  loop :  0.04 (0.23), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F 396 
 TYR   0.028   0.002   TYR A 548 
 PHE   0.016   0.002   PHE F 212 
 TRP   0.021   0.002   TRP A 776 
 HIS   0.005   0.001   HIS A 677 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.18 (16368)
  covalent geometry    : angle       0.63193 /  0.34 (22222)
  SS BOND              : bond        0.00074 /  0.05 (    1)
  SS BOND              : angle       0.98723 /  0.43 (    2)
  hydrogen bonds       : bond        0.04739 /  3.26 (  796)
  hydrogen bonds       : angle       5.40829 /  3.84 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 142
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9552 (ptpt) cc_final: 0.9207 (pttm)
REVERT: A  304 MET cc_start: 0.9678 (mmp) cc_final: 0.9415 (mmp)
REVERT: A  372 MET cc_start: 0.9089 (mmm) cc_final: 0.8823 (mmm)
REVERT: B  165 HIS cc_start: 0.9093 (t70) cc_final: 0.8376 (t70)
REVERT: B  244 LEU cc_start: 0.9435 (mt) cc_final: 0.8994 (mt)
REVERT: B  263 TYR cc_start: 0.9523 (t80) cc_final: 0.9309 (t80)
REVERT: B  306 MET cc_start: 0.7778 (mpp) cc_final: 0.7415 (mpp)
REVERT: B  346 LEU cc_start: 0.9664 (tp) cc_final: 0.9393 (tp)
REVERT: C   99 PHE cc_start: 0.8663 (p90) cc_final: 0.8437 (p90)
REVERT: C  155 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8996 (pm20)
REVERT: C  157 TYR cc_start: 0.9504 (m-80) cc_final: 0.9050 (m-80)
REVERT: C  203 ASN cc_start: 0.9464 (p0) cc_final: 0.8960 (p0)
REVERT: D   74 ASP cc_start: 0.9224 (m-30) cc_final: 0.8862 (m-30)
REVERT: E  105 ASP cc_start: 0.9167 (t0) cc_final: 0.8893 (t0)
REVERT: F   71 MET cc_start: 0.9223 (ptt) cc_final: 0.8852 (ptt)
REVERT: F  128 TYR cc_start: 0.9504 (t80) cc_final: 0.9160 (t80)
REVERT: F  223 GLN cc_start: 0.8751 (mp-120) cc_final: 0.8389 (pp30)
  outliers start: 4
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1281
  time to fit residues: 28.2052
Evaluate side-chains
  112 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [60, 19, 16, 162, 114, 94, 11, 95, 166, 40, 108]
   chunk 60 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    8.9990
   chunk 162 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 166 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 108 optimal weight:   10.0000
   overall best weight:    4.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.052691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.034330 restraints weight = 127971.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035496 restraints weight = 72446.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.036293 restraints weight = 50559.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.036837 restraints weight = 40058.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.037134 restraints weight = 34461.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073  16369  Z= 0.205
  Angle     :  0.609   7.905  22224  Z= 0.326
  Chirality :  0.042   0.208   2446
  Planarity :  0.004   0.051   2940
  Dihedral  :  4.605  49.563   2247
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.69 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  3.20 %
    Favored  : 96.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.18), residues: 2047
  helix:  1.68 (0.20), residues: 619
  sheet:  0.40 (0.20), residues: 583
  loop :  0.02 (0.22), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 396 
 TYR   0.025   0.002   TYR A 548 
 PHE   0.018   0.001   PHE A  67 
 TRP   0.022   0.002   TRP A 546 
 HIS   0.009   0.002   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.21 (16368)
  covalent geometry    : angle       0.60870 /  0.33 (22222)
  SS BOND              : bond        0.00040 /  0.02 (    1)
  SS BOND              : angle       0.54884 /  0.25 (    2)
  hydrogen bonds       : bond        0.04485 /  3.07 (  796)
  hydrogen bonds       : angle       5.22723 /  3.72 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.9717 (mmp) cc_final: 0.9433 (mmm)
REVERT: A  372 MET cc_start: 0.9267 (mmm) cc_final: 0.8978 (mmm)
REVERT: B  244 LEU cc_start: 0.9458 (mt) cc_final: 0.8902 (mt)
REVERT: B  263 TYR cc_start: 0.9406 (t80) cc_final: 0.9076 (t80)
REVERT: B  306 MET cc_start: 0.7754 (mpp) cc_final: 0.7485 (mpp)
REVERT: B  346 LEU cc_start: 0.9664 (tp) cc_final: 0.9397 (tp)
REVERT: C   99 PHE cc_start: 0.8688 (p90) cc_final: 0.8431 (p90)
REVERT: C  203 ASN cc_start: 0.9393 (p0) cc_final: 0.8861 (p0)
REVERT: D   74 ASP cc_start: 0.9225 (m-30) cc_final: 0.8867 (m-30)
REVERT: D  154 TYR cc_start: 0.8818 (m-10) cc_final: 0.8559 (m-10)
REVERT: E   31 ASP cc_start: 0.8976 (m-30) cc_final: 0.8742 (m-30)
REVERT: E  105 ASP cc_start: 0.9178 (t0) cc_final: 0.8852 (t0)
REVERT: F   71 MET cc_start: 0.9258 (ptt) cc_final: 0.8952 (ptt)
REVERT: F  128 TYR cc_start: 0.9510 (t80) cc_final: 0.9175 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 131
  average time/residue: 0.1239
  time to fit residues: 24.5333
Evaluate side-chains
  102 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [163, 102, 196, 88, 76, 95, 24, 157, 22, 170, 87]
   chunk 163 optimal weight:    0.6980
   chunk 102 optimal weight:    6.9990
   chunk 196 optimal weight:   30.0000
   chunk 88 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0980
   chunk 24 optimal weight:   10.0000
   chunk 157 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 170 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 542 GLN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.053429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.034943 restraints weight = 125388.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.036184 restraints weight = 70743.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036999 restraints weight = 49548.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.037468 restraints weight = 39201.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.037866 restraints weight = 34091.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  16369  Z= 0.125
  Angle     :  0.546   7.707  22224  Z= 0.292
  Chirality :  0.042   0.197   2446
  Planarity :  0.003   0.049   2940
  Dihedral  :  4.469  50.413   2247
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.15 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.79 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.19), residues: 2047
  helix:  1.76 (0.20), residues: 620
  sheet:  0.37 (0.21), residues: 585
  loop :  0.10 (0.23), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 160 
 TYR   0.018   0.001   TYR A 548 
 PHE   0.018   0.001   PHE B 104 
 TRP   0.017   0.001   TRP A 546 
 HIS   0.006   0.001   HIS B  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (16368)
  covalent geometry    : angle       0.54594 /  0.29 (22222)
  SS BOND              : bond        0.00063 /  0.04 (    1)
  SS BOND              : angle       0.54979 /  0.25 (    2)
  hydrogen bonds       : bond        0.04002 /  2.73 (  796)
  hydrogen bonds       : angle       4.99040 /  3.54 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.9699 (mmp) cc_final: 0.9447 (mmm)
REVERT: A  372 MET cc_start: 0.9273 (mmm) cc_final: 0.8875 (mmm)
REVERT: B  244 LEU cc_start: 0.9440 (mt) cc_final: 0.8952 (mt)
REVERT: B  263 TYR cc_start: 0.9451 (t80) cc_final: 0.9161 (t80)
REVERT: B  306 MET cc_start: 0.7791 (mpp) cc_final: 0.7504 (mpp)
REVERT: B  346 LEU cc_start: 0.9664 (tp) cc_final: 0.9387 (tp)
REVERT: C   56 MET cc_start: 0.8253 (tpt) cc_final: 0.7782 (mmm)
REVERT: C   99 PHE cc_start: 0.8434 (p90) cc_final: 0.8152 (p90)
REVERT: C  153 GLU cc_start: 0.8483 (tp30) cc_final: 0.8267 (tp30)
REVERT: C  155 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8914 (pm20)
REVERT: C  157 TYR cc_start: 0.9479 (m-80) cc_final: 0.9090 (m-80)
REVERT: C  201 MET cc_start: 0.9594 (tpt) cc_final: 0.9390 (mmm)
REVERT: C  202 MET cc_start: 0.9323 (tmm) cc_final: 0.8838 (tmm)
REVERT: C  203 ASN cc_start: 0.9409 (p0) cc_final: 0.8861 (p0)
REVERT: D   74 ASP cc_start: 0.9171 (m-30) cc_final: 0.8808 (m-30)
REVERT: D  154 TYR cc_start: 0.8740 (m-10) cc_final: 0.8467 (m-10)
REVERT: E   31 ASP cc_start: 0.8913 (m-30) cc_final: 0.8642 (m-30)
REVERT: E  105 ASP cc_start: 0.9152 (t0) cc_final: 0.8867 (t0)
REVERT: F   71 MET cc_start: 0.9211 (ptt) cc_final: 0.8853 (ptt)
REVERT: F  128 TYR cc_start: 0.9496 (t80) cc_final: 0.9164 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1256
  time to fit residues: 25.5640
Evaluate side-chains
  106 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [17, 90, 9, 13, 28, 102, 164, 54, 182, 49, 140]
   chunk 17 optimal weight:   10.0000
   chunk 90 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:    0.3980
   chunk 28 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 164 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 182 optimal weight:   50.0000
   chunk 49 optimal weight:    9.9990
   chunk 140 optimal weight:    3.9990
   overall best weight:    3.6788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  40 GLN
F 113 GLN
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.052604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.034201 restraints weight = 126560.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.035357 restraints weight = 72791.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.036164 restraints weight = 51054.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.036687 restraints weight = 40592.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.037049 restraints weight = 35054.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16369  Z= 0.173
  Angle     :  0.568   7.378  22224  Z= 0.304
  Chirality :  0.042   0.183   2446
  Planarity :  0.004   0.050   2940
  Dihedral  :  4.484  54.335   2247
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.74 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.19), residues: 2047
  helix:  1.74 (0.20), residues: 620
  sheet:  0.28 (0.20), residues: 587
  loop :  0.07 (0.22), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 366 
 TYR   0.024   0.001   TYR A 548 
 PHE   0.017   0.001   PHE B 104 
 TRP   0.021   0.001   TRP A 546 
 HIS   0.007   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.17 (16368)
  covalent geometry    : angle       0.56848 /  0.30 (22222)
  SS BOND              : bond        0.00042 /  0.03 (    1)
  SS BOND              : angle       0.42342 /  0.20 (    2)
  hydrogen bonds       : bond        0.03992 /  2.72 (  796)
  hydrogen bonds       : angle       4.99329 /  3.54 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.647 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9600 (ptpt) cc_final: 0.9356 (pttm)
REVERT: A  304 MET cc_start: 0.9727 (mmp) cc_final: 0.9457 (mmm)
REVERT: A  372 MET cc_start: 0.9327 (mmm) cc_final: 0.9023 (mmm)
REVERT: B  244 LEU cc_start: 0.9447 (mt) cc_final: 0.8892 (mt)
REVERT: B  263 TYR cc_start: 0.9453 (t80) cc_final: 0.9160 (t80)
REVERT: B  278 MET cc_start: 0.9307 (mpp) cc_final: 0.9010 (mpp)
REVERT: B  306 MET cc_start: 0.7789 (mpp) cc_final: 0.7505 (mpp)
REVERT: B  346 LEU cc_start: 0.9671 (tp) cc_final: 0.9410 (tp)
REVERT: C   56 MET cc_start: 0.8299 (tpt) cc_final: 0.7841 (mmm)
REVERT: C   99 PHE cc_start: 0.8492 (p90) cc_final: 0.8194 (p90)
REVERT: C  106 LEU cc_start: 0.9647 (tp) cc_final: 0.9435 (tp)
REVERT: C  153 GLU cc_start: 0.8576 (tp30) cc_final: 0.8336 (tp30)
REVERT: C  155 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8880 (pm20)
REVERT: C  157 TYR cc_start: 0.9509 (m-80) cc_final: 0.9101 (m-80)
REVERT: C  201 MET cc_start: 0.9616 (tpt) cc_final: 0.9373 (mmm)
REVERT: C  203 ASN cc_start: 0.9376 (p0) cc_final: 0.9067 (p0)
REVERT: D   74 ASP cc_start: 0.9197 (m-30) cc_final: 0.8844 (m-30)
REVERT: D  154 TYR cc_start: 0.8789 (m-10) cc_final: 0.8477 (m-10)
REVERT: E   31 ASP cc_start: 0.8950 (m-30) cc_final: 0.8748 (t0)
REVERT: E  105 ASP cc_start: 0.9171 (t0) cc_final: 0.8862 (t0)
REVERT: F   71 MET cc_start: 0.9238 (ptt) cc_final: 0.8879 (ptt)
REVERT: F  128 TYR cc_start: 0.9498 (t80) cc_final: 0.9176 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1230
  time to fit residues: 24.6823
Evaluate side-chains
  103 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [36, 174, 111, 12, 55, 14, 191, 194, 24, 163, 129]
   chunk 36 optimal weight:    3.9990
   chunk 174 optimal weight:    9.9990
   chunk 111 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 191 optimal weight:    9.9990
   chunk 194 optimal weight:    0.0050
   chunk 24 optimal weight:    6.9990
   chunk 163 optimal weight:    0.7980
   chunk 129 optimal weight:   20.0000
   overall best weight:    4.1600

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.052193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.034052 restraints weight = 129183.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.035192 restraints weight = 72948.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.035984 restraints weight = 50842.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036514 restraints weight = 40249.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.036824 restraints weight = 34636.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  16369  Z= 0.187
  Angle     :  0.578  12.438  22224  Z= 0.308
  Chirality :  0.042   0.167   2446
  Planarity :  0.004   0.063   2940
  Dihedral  :  4.548  56.199   2247
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.54 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.63 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.18), residues: 2047
  helix:  1.72 (0.20), residues: 620
  sheet:  0.25 (0.21), residues: 577
  loop :  0.03 (0.22), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  25 
 TYR   0.034   0.002   TYR F 398 
 PHE   0.019   0.001   PHE B 104 
 TRP   0.047   0.002   TRP B 228 
 HIS   0.007   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.19 (16368)
  covalent geometry    : angle       0.57783 /  0.31 (22222)
  SS BOND              : bond        0.00054 /  0.03 (    1)
  SS BOND              : angle       0.39533 /  0.19 (    2)
  hydrogen bonds       : bond        0.04093 /  2.81 (  796)
  hydrogen bonds       : angle       5.00706 /  3.55 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.9728 (mmp) cc_final: 0.9458 (mmm)
REVERT: A  372 MET cc_start: 0.9355 (mmm) cc_final: 0.9067 (mmm)
REVERT: A  717 GLU cc_start: 0.8573 (pp20) cc_final: 0.8160 (pp20)
REVERT: B  244 LEU cc_start: 0.9456 (mt) cc_final: 0.8919 (mt)
REVERT: B  263 TYR cc_start: 0.9473 (t80) cc_final: 0.9200 (t80)
REVERT: B  278 MET cc_start: 0.9345 (mpp) cc_final: 0.8812 (mpp)
REVERT: B  306 MET cc_start: 0.7806 (mpp) cc_final: 0.7549 (mpp)
REVERT: B  346 LEU cc_start: 0.9655 (tp) cc_final: 0.9399 (tp)
REVERT: C   56 MET cc_start: 0.8342 (tpt) cc_final: 0.7886 (mmm)
REVERT: C   99 PHE cc_start: 0.8492 (p90) cc_final: 0.8192 (p90)
REVERT: C  106 LEU cc_start: 0.9597 (tp) cc_final: 0.9380 (tp)
REVERT: C  153 GLU cc_start: 0.8625 (tp30) cc_final: 0.8321 (tp30)
REVERT: C  155 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8851 (pm20)
REVERT: C  157 TYR cc_start: 0.9533 (m-80) cc_final: 0.9114 (m-80)
REVERT: C  201 MET cc_start: 0.9641 (tpt) cc_final: 0.9400 (mmm)
REVERT: C  203 ASN cc_start: 0.9361 (p0) cc_final: 0.9052 (p0)
REVERT: D   74 ASP cc_start: 0.9203 (m-30) cc_final: 0.8853 (m-30)
REVERT: D  154 TYR cc_start: 0.8834 (m-10) cc_final: 0.8495 (m-10)
REVERT: E   31 ASP cc_start: 0.8847 (m-30) cc_final: 0.8511 (m-30)
REVERT: E   50 MET cc_start: 0.9132 (mtt) cc_final: 0.8741 (mtt)
REVERT: E   80 GLN cc_start: 0.9583 (tt0) cc_final: 0.8964 (tp-100)
REVERT: E  105 ASP cc_start: 0.9182 (t0) cc_final: 0.8895 (t0)
REVERT: F   71 MET cc_start: 0.9250 (ptt) cc_final: 0.8922 (ptt)
REVERT: F   83 MET cc_start: 0.9557 (tpt) cc_final: 0.9353 (tpt)
REVERT: F  128 TYR cc_start: 0.9510 (t80) cc_final: 0.9189 (t80)
REVERT: F  402 MET cc_start: 0.9479 (tmm) cc_final: 0.9138 (ptt)
  outliers start: 1
  outliers final: 1
  residues processed: 127
  average time/residue: 0.1328
  time to fit residues: 25.2857
Evaluate side-chains
  104 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [18, 148, 43, 77, 163, 28, 49, 152, 108, 120, 0]
   chunk 18 optimal weight:   20.0000
   chunk 148 optimal weight:    0.8980
   chunk 43 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 163 optimal weight:   20.0000
   chunk 28 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 152 optimal weight:    0.6980
   chunk 108 optimal weight:    0.5980
   chunk 120 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 542 GLN
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  33 ASN
F 113 GLN
** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.053265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035128 restraints weight = 127828.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036315 restraints weight = 71585.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.037094 restraints weight = 49783.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 64)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.037648 restraints weight = 39742.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037861 restraints weight = 34213.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  16369  Z= 0.108
  Angle     :  0.526   8.448  22224  Z= 0.280
  Chirality :  0.042   0.171   2446
  Planarity :  0.004   0.068   2940
  Dihedral  :  4.385  57.264   2247
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.39 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.87 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.19), residues: 2047
  helix:  1.88 (0.20), residues: 621
  sheet:  0.20 (0.21), residues: 581
  loop :  0.11 (0.22), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 160 
 TYR   0.022   0.001   TYR A 548 
 PHE   0.023   0.001   PHE A  67 
 TRP   0.016   0.001   TRP A 546 
 HIS   0.005   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.11 (16368)
  covalent geometry    : angle       0.52627 /  0.28 (22222)
  SS BOND              : bond        0.00048 /  0.03 (    1)
  SS BOND              : angle       0.46180 /  0.20 (    2)
  hydrogen bonds       : bond        0.03698 /  2.55 (  796)
  hydrogen bonds       : angle       4.75024 /  3.36 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9593 (ptpt) cc_final: 0.9344 (pttm)
REVERT: A  304 MET cc_start: 0.9694 (mmp) cc_final: 0.9447 (mmm)
REVERT: A  372 MET cc_start: 0.9338 (mmm) cc_final: 0.9071 (mmm)
REVERT: A  717 GLU cc_start: 0.8552 (pp20) cc_final: 0.8150 (pp20)
REVERT: B  244 LEU cc_start: 0.9431 (mt) cc_final: 0.8945 (mt)
REVERT: B  263 TYR cc_start: 0.9499 (t80) cc_final: 0.9221 (t80)
REVERT: B  278 MET cc_start: 0.9390 (mpp) cc_final: 0.8851 (mpp)
REVERT: B  306 MET cc_start: 0.7814 (mpp) cc_final: 0.7491 (mpp)
REVERT: B  346 LEU cc_start: 0.9683 (tp) cc_final: 0.9415 (tp)
REVERT: C   56 MET cc_start: 0.8261 (tpt) cc_final: 0.7910 (mmm)
REVERT: C   99 PHE cc_start: 0.8512 (p90) cc_final: 0.8192 (p90)
REVERT: C  106 LEU cc_start: 0.9577 (tp) cc_final: 0.9339 (tp)
REVERT: C  155 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8911 (pm20)
REVERT: C  201 MET cc_start: 0.9608 (tpt) cc_final: 0.9372 (mmm)
REVERT: C  203 ASN cc_start: 0.9359 (p0) cc_final: 0.9050 (p0)
REVERT: D   74 ASP cc_start: 0.9115 (m-30) cc_final: 0.8766 (m-30)
REVERT: D  109 MET cc_start: 0.9599 (mtp) cc_final: 0.9017 (ttt)
REVERT: D  154 TYR cc_start: 0.8720 (m-10) cc_final: 0.8416 (m-10)
REVERT: E   31 ASP cc_start: 0.8864 (m-30) cc_final: 0.8532 (m-30)
REVERT: E   80 GLN cc_start: 0.9578 (tt0) cc_final: 0.8932 (tm-30)
REVERT: E  105 ASP cc_start: 0.9183 (t0) cc_final: 0.8920 (t0)
REVERT: F   71 MET cc_start: 0.9241 (ptt) cc_final: 0.8883 (ptt)
REVERT: F  128 TYR cc_start: 0.9491 (t80) cc_final: 0.9181 (t80)
REVERT: F  402 MET cc_start: 0.9472 (tmm) cc_final: 0.9157 (ptt)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1249
  time to fit residues: 26.1604
Evaluate side-chains
  106 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [44, 64, 121, 128, 198, 89, 176, 199, 185, 53, 202]
   chunk 44 optimal weight:   20.0000
   chunk 64 optimal weight:    0.2980
   chunk 121 optimal weight:   10.0000
   chunk 128 optimal weight:    7.9990
   chunk 198 optimal weight:   30.0000
   chunk 89 optimal weight:    2.9990
   chunk 176 optimal weight:    2.9990
   chunk 199 optimal weight:   10.0000
   chunk 185 optimal weight:   20.0000
   chunk 53 optimal weight:   40.0000
   chunk 202 optimal weight:   10.0000
   overall best weight:    4.8590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN
F 237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.051622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.033618 restraints weight = 132996.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034756 restraints weight = 74976.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035529 restraints weight = 52643.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.036011 restraints weight = 42017.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.036344 restraints weight = 36557.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16369  Z= 0.211
  Angle     :  0.604   9.785  22224  Z= 0.321
  Chirality :  0.042   0.167   2446
  Planarity :  0.004   0.068   2940
  Dihedral  :  4.590  63.425   2247
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.93 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.18), residues: 2047
  helix:  1.69 (0.20), residues: 619
  sheet:  0.14 (0.21), residues: 574
  loop : -0.09 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  25 
 TYR   0.027   0.002   TYR A 548 
 PHE   0.020   0.002   PHE A  67 
 TRP   0.028   0.002   TRP A 546 
 HIS   0.007   0.002   HIS D 102 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.21 (16368)
  covalent geometry    : angle       0.60393 /  0.32 (22222)
  SS BOND              : bond        0.00058 /  0.04 (    1)
  SS BOND              : angle       0.38942 /  0.18 (    2)
  hydrogen bonds       : bond        0.04078 /  2.80 (  796)
  hydrogen bonds       : angle       4.98371 /  3.54 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9610 (ptpt) cc_final: 0.9405 (ptpp)
REVERT: A  304 MET cc_start: 0.9748 (mmp) cc_final: 0.9494 (mmm)
REVERT: A  372 MET cc_start: 0.9378 (mmm) cc_final: 0.9134 (mmm)
REVERT: A  717 GLU cc_start: 0.8572 (pp20) cc_final: 0.8272 (pp20)
REVERT: B  244 LEU cc_start: 0.9465 (mt) cc_final: 0.8926 (mt)
REVERT: B  278 MET cc_start: 0.9368 (mpp) cc_final: 0.9066 (mpp)
REVERT: B  346 LEU cc_start: 0.9644 (tp) cc_final: 0.9392 (tp)
REVERT: C   56 MET cc_start: 0.8416 (tpt) cc_final: 0.7952 (mmm)
REVERT: C   99 PHE cc_start: 0.8555 (p90) cc_final: 0.8241 (p90)
REVERT: C  106 LEU cc_start: 0.9583 (tp) cc_final: 0.9363 (tp)
REVERT: C  153 GLU cc_start: 0.8659 (tp30) cc_final: 0.8151 (tp30)
REVERT: C  155 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8836 (pm20)
REVERT: C  157 TYR cc_start: 0.9569 (m-80) cc_final: 0.9151 (m-80)
REVERT: C  201 MET cc_start: 0.9629 (tpt) cc_final: 0.9393 (mmm)
REVERT: C  203 ASN cc_start: 0.9370 (p0) cc_final: 0.9064 (p0)
REVERT: D   74 ASP cc_start: 0.9193 (m-30) cc_final: 0.8838 (m-30)
REVERT: D  154 TYR cc_start: 0.8821 (m-10) cc_final: 0.8478 (m-10)
REVERT: E   31 ASP cc_start: 0.8946 (m-30) cc_final: 0.8676 (m-30)
REVERT: E   50 MET cc_start: 0.9134 (mtt) cc_final: 0.8766 (mtt)
REVERT: E  105 ASP cc_start: 0.9161 (t0) cc_final: 0.8900 (t0)
REVERT: F   71 MET cc_start: 0.9261 (ptt) cc_final: 0.8939 (ptt)
REVERT: F  114 MET cc_start: 0.9539 (mmt) cc_final: 0.9188 (mmt)
REVERT: F  128 TYR cc_start: 0.9524 (t80) cc_final: 0.9229 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1315
  time to fit residues: 24.1744
Evaluate side-chains
  102 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [145, 3, 162, 111, 58, 161, 185, 113, 10, 99, 105]
   chunk 145 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 162 optimal weight:    3.9990
   chunk 111 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 161 optimal weight:    0.1980
   chunk 185 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    3.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.051841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.033706 restraints weight = 130961.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.034839 restraints weight = 74372.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035585 restraints weight = 51877.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.036093 restraints weight = 41478.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036377 restraints weight = 35994.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16369  Z= 0.158
  Angle     :  0.567  11.263  22224  Z= 0.302
  Chirality :  0.042   0.192   2446
  Planarity :  0.004   0.068   2940
  Dihedral  :  4.562  62.642   2247
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.83 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.18), residues: 2047
  helix:  1.66 (0.20), residues: 621
  sheet:  0.10 (0.21), residues: 578
  loop : -0.05 (0.22), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 223 
 TYR   0.029   0.002   TYR F 398 
 PHE   0.023   0.001   PHE A  67 
 TRP   0.023   0.001   TRP A 546 
 HIS   0.006   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.16 (16368)
  covalent geometry    : angle       0.56747 /  0.30 (22222)
  SS BOND              : bond        0.00032 /  0.02 (    1)
  SS BOND              : angle       0.35855 /  0.16 (    2)
  hydrogen bonds       : bond        0.03923 /  2.68 (  796)
  hydrogen bonds       : angle       4.90527 /  3.48 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.9619 (ptpt) cc_final: 0.9388 (pttm)
REVERT: A  304 MET cc_start: 0.9754 (mmp) cc_final: 0.9502 (mmm)
REVERT: A  372 MET cc_start: 0.9383 (mmm) cc_final: 0.9138 (mmm)
REVERT: A  717 GLU cc_start: 0.8576 (pp20) cc_final: 0.8249 (pp20)
REVERT: B  244 LEU cc_start: 0.9486 (mt) cc_final: 0.8982 (mt)
REVERT: B  278 MET cc_start: 0.9389 (mpp) cc_final: 0.8874 (mpp)
REVERT: B  346 LEU cc_start: 0.9652 (tp) cc_final: 0.9398 (tp)
REVERT: C   56 MET cc_start: 0.8399 (tpt) cc_final: 0.7934 (mmm)
REVERT: C   99 PHE cc_start: 0.8545 (p90) cc_final: 0.8241 (p90)
REVERT: C  106 LEU cc_start: 0.9587 (tp) cc_final: 0.9373 (tp)
REVERT: C  153 GLU cc_start: 0.8587 (tp30) cc_final: 0.8140 (tp30)
REVERT: C  155 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8853 (pm20)
REVERT: C  157 TYR cc_start: 0.9563 (m-80) cc_final: 0.9113 (m-80)
REVERT: C  203 ASN cc_start: 0.9372 (p0) cc_final: 0.9102 (p0)
REVERT: D   74 ASP cc_start: 0.9185 (m-30) cc_final: 0.8827 (m-30)
REVERT: D  111 MET cc_start: 0.9730 (mmm) cc_final: 0.9516 (mmm)
REVERT: D  154 TYR cc_start: 0.8807 (m-10) cc_final: 0.8446 (m-10)
REVERT: E   31 ASP cc_start: 0.8947 (m-30) cc_final: 0.8747 (t0)
REVERT: E   50 MET cc_start: 0.9148 (mtt) cc_final: 0.8741 (mtt)
REVERT: E  105 ASP cc_start: 0.9231 (t0) cc_final: 0.8958 (t0)
REVERT: F   71 MET cc_start: 0.9247 (ptt) cc_final: 0.8939 (ptt)
REVERT: F  128 TYR cc_start: 0.9517 (t80) cc_final: 0.9225 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1218
  time to fit residues: 22.5550
Evaluate side-chains
  102 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [7, 200, 190, 116, 171, 97, 28, 35, 5, 56, 149]
   chunk 7 optimal weight:    7.9990
   chunk 200 optimal weight:    5.9990
   chunk 190 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 171 optimal weight:    3.9990
   chunk 97 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.052051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.033885 restraints weight = 128599.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.035022 restraints weight = 72735.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.035819 restraints weight = 50852.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036314 restraints weight = 40412.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.036666 restraints weight = 34974.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16369  Z= 0.139
  Angle     :  0.553   9.635  22224  Z= 0.295
  Chirality :  0.042   0.165   2446
  Planarity :  0.004   0.045   2940
  Dihedral  :  4.544  64.336   2247
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.78 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.19), residues: 2047
  helix:  1.72 (0.20), residues: 618
  sheet:  0.08 (0.21), residues: 587
  loop : -0.03 (0.22), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 223 
 TYR   0.024   0.001   TYR A 548 
 PHE   0.021   0.001   PHE B 104 
 TRP   0.021   0.001   TRP A 546 
 HIS   0.006   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 (16368)
  covalent geometry    : angle       0.55312 /  0.29 (22222)
  SS BOND              : bond        0.00051 /  0.03 (    1)
  SS BOND              : angle       0.42438 /  0.19 (    2)
  hydrogen bonds       : bond        0.03824 /  2.63 (  796)
  hydrogen bonds       : angle       4.84753 /  3.44 ( 2223)

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

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

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4094 Ramachandran restraints generated.
    2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 TYR cc_start: 0.8628 (t80) cc_final: 0.8307 (t80)
REVERT: A  303 LYS cc_start: 0.9617 (ptpt) cc_final: 0.9381 (pttm)
REVERT: A  304 MET cc_start: 0.9754 (mmp) cc_final: 0.9511 (mmm)
REVERT: A  372 MET cc_start: 0.9383 (mmm) cc_final: 0.9156 (mmm)
REVERT: A  717 GLU cc_start: 0.8599 (pp20) cc_final: 0.8267 (pp20)
REVERT: B  244 LEU cc_start: 0.9498 (mt) cc_final: 0.9009 (mt)
REVERT: B  278 MET cc_start: 0.9411 (mpp) cc_final: 0.8871 (mpp)
REVERT: B  346 LEU cc_start: 0.9653 (tp) cc_final: 0.9407 (tp)
REVERT: C   99 PHE cc_start: 0.8619 (p90) cc_final: 0.8303 (p90)
REVERT: C  106 LEU cc_start: 0.9596 (tp) cc_final: 0.9387 (tp)
REVERT: C  153 GLU cc_start: 0.8631 (tp30) cc_final: 0.8250 (tp30)
REVERT: C  155 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8872 (pm20)
REVERT: C  203 ASN cc_start: 0.9385 (p0) cc_final: 0.9113 (p0)
REVERT: D   74 ASP cc_start: 0.9182 (m-30) cc_final: 0.8821 (m-30)
REVERT: D  111 MET cc_start: 0.9746 (mmm) cc_final: 0.9531 (mmm)
REVERT: D  154 TYR cc_start: 0.8802 (m-10) cc_final: 0.8452 (m-10)
REVERT: D  225 MET cc_start: 0.9166 (mmm) cc_final: 0.8857 (mmm)
REVERT: E   50 MET cc_start: 0.9125 (mtt) cc_final: 0.8728 (mtt)
REVERT: E  105 ASP cc_start: 0.9239 (t0) cc_final: 0.8985 (t0)
REVERT: F   71 MET cc_start: 0.9243 (ptt) cc_final: 0.8944 (ptt)
REVERT: F  128 TYR cc_start: 0.9521 (t80) cc_final: 0.9238 (t80)
REVERT: F  402 MET cc_start: 0.9473 (tmm) cc_final: 0.9187 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1243
  time to fit residues: 23.0728
Evaluate side-chains
  100 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks: [129, 12, 156, 1, 34, 163, 193, 180, 173, 58, 125]
   chunk 129 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 156 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0060
   chunk 34 optimal weight:    0.9990
   chunk 163 optimal weight:    0.9980
   chunk 193 optimal weight:    4.9990
   chunk 180 optimal weight:    6.9990
   chunk 173 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 125 optimal weight:   30.0000
   overall best weight:    2.8002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.051843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.033810 restraints weight = 128810.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.034895 restraints weight = 73234.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035675 restraints weight = 51477.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.036183 restraints weight = 41134.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.036505 restraints weight = 35661.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16369  Z= 0.140
  Angle     :  0.562   8.999  22224  Z= 0.298
  Chirality :  0.043   0.305   2446
  Planarity :  0.004   0.045   2940
  Dihedral  :  4.558  66.013   2247
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.83 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.19), residues: 2047
  helix:  1.77 (0.20), residues: 618
  sheet:  0.07 (0.21), residues: 586
  loop : -0.02 (0.22), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 223 
 TYR   0.024   0.001   TYR A 548 
 PHE   0.020   0.001   PHE B 104 
 TRP   0.022   0.001   TRP A 546 
 HIS   0.006   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 (16368)
  covalent geometry    : angle       0.56156 /  0.30 (22222)
  SS BOND              : bond        0.00045 /  0.03 (    1)
  SS BOND              : angle       0.41115 /  0.19 (    2)
  hydrogen bonds       : bond        0.03792 /  2.61 (  796)
  hydrogen bonds       : angle       4.82219 /  3.42 ( 2223)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3021.06 seconds
wall clock time: 52 minutes 47.40 seconds (3167.40 seconds total)