Starting phenix.real_space_refine
on Fri Jul  3 15:18:11 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g3l_29701/07_2026/8g3l_29701.map"
  }
  resolution = 3.5
  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=   0.020
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      62      5.16       5
     C    9385      2.51       5
     N    2374      2.21       5
     O    2619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14442
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5000
          Classifications: {'peptide': 635}
          Link IDs: {'PTRANS': 10, 'TRANS': 624}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1915
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 5, 'TRANS': 238}
    Chain: "C"
      Number of atoms: 1915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1915
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 5, 'TRANS': 238}
    Chain: "D"
      Number of atoms: 2738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2738
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 324}
    Chain: "E"
      Number of atoms: 2738
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2738
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 324}
    Chain: "A"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 116
          Unusual residues: {'6OU': 2, 'PLM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'OLA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.90, per 1000 atoms: 0.20
  Number of scatterers: 14442
  At special positions: 0
  Unit cell: (93.304, 117.72, 197.072, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     P       2     15.00
     O    2619      8.00
     N    2374      7.00
     C    9385      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.93
  Conformation dependent library (CDL) restraints added in 447.9 milliseconds
  

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 12 sheets defined
      60.6% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 4.049A  pdb=" N   LEU A   6 " --> pdb=" O   ASN A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 41
      removed outlier: 3.665A  pdb=" N   TYR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.741A  pdb=" N   VAL A  47 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 82
      removed outlier: 3.974A  pdb=" N   THR A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LYS A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ARG A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 94
      removed outlier: 3.626A  pdb=" N   GLY A  94 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 122
    Processing helix  chain 'A' and resid 126 through 139
      removed outlier: 3.632A  pdb=" N   ILE A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 178
      removed outlier: 3.944A  pdb=" N   LEU A 153 " --> pdb=" O   SER A 149 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 159 " --> pdb=" O   GLN A 155 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   PHE A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 220
      removed outlier: 4.031A  pdb=" N   GLY A 205 " --> pdb=" O   GLN A 201 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ILE A 209 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 213 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A 216 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 253
    Processing helix  chain 'A' and resid 254 through 265
    Processing helix  chain 'A' and resid 272 through 286
      removed outlier: 3.566A  pdb=" N   VAL A 276 " --> pdb=" O   ASN A 272 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   SER A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   SER A 281 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   MET A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   PHE A 284 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   MET A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 316
      removed outlier: 3.783A  pdb=" N   TYR A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR A 315 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   SER A 316 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 325
      removed outlier: 3.538A  pdb=" N   VAL A 325 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 346
      removed outlier: 3.905A  pdb=" N   GLU A 346 " --> pdb=" O   ASN A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.616A  pdb=" N   MET A 369 " --> pdb=" O   ALA A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.585A  pdb=" N   GLN A 413 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS A 414 " --> pdb=" O   ASP A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 472
      removed outlier: 3.835A  pdb=" N   GLN A 467 " --> pdb=" O   SER A 463 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LYS A 470 " --> pdb=" O   LYS A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 518 through 557
      removed outlier: 3.622A  pdb=" N   LYS A 549 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLN A 550 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   MET A 551 " --> pdb=" O   TYR A 547 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   GLY A 552 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 557 " --> pdb=" O   GLU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 565
    Processing helix  chain 'A' and resid 570 through 602
      removed outlier: 3.856A  pdb=" N   ILE A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ILE A 588 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      Proline residue:  A 589  - end of helix
    Processing helix  chain 'A' and resid 614 through 633
      removed outlier: 3.960A  pdb=" N   MET A 618 " --> pdb=" O   ALA A 614 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A 629 " --> pdb=" O   ALA A 625 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   PHE A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   GLY A 631 " --> pdb=" O   TYR A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 644
      removed outlier: 4.234A  pdb=" N   TYR A 637 " --> pdb=" O   LEU A 633 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   SER A 644 " --> pdb=" O   LYS A 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 3.533A  pdb=" N   SER B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 86
    Processing helix  chain 'B' and resid 101 through 108
    Processing helix  chain 'B' and resid 109 through 112
      removed outlier: 3.894A  pdb=" N   ILE B 112 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 109 through 112'
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 133 through 137
      removed outlier: 3.931A  pdb=" N   ARG B 137 " --> pdb=" O   TYR B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
    Processing helix  chain 'B' and resid 145 through 158
      removed outlier: 3.644A  pdb=" N   LYS B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLN B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 193
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 231 through 246
    Processing helix  chain 'C' and resid 45 through 55
    Processing helix  chain 'C' and resid 75 through 86
    Processing helix  chain 'C' and resid 101 through 108
    Processing helix  chain 'C' and resid 109 through 111
      No H-bonds generated for 'chain 'C' and resid 109 through 111'
    Processing helix  chain 'C' and resid 116 through 132
      removed outlier: 3.527A  pdb=" N   ALA C 120 " --> pdb=" O   SER C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 157
      removed outlier: 3.673A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 193
      removed outlier: 3.609A  pdb=" N   GLN C 191 " --> pdb=" O   SER C 187 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS C 192 " --> pdb=" O   GLN C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 208
      removed outlier: 3.794A  pdb=" N   ALA C 207 " --> pdb=" O   ASP C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 246
    Processing helix  chain 'D' and resid 2 through 9
    Processing helix  chain 'D' and resid 11 through 30
      removed outlier: 3.695A  pdb=" N   ALA D  15 " --> pdb=" O   SER D  11 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA D  27 " --> pdb=" O   MET D  23 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ASP D  30 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 61
      removed outlier: 3.869A  pdb=" N   VAL D  38 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU D  47 " --> pdb=" O   TYR D  43 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE D  50 " --> pdb=" O   ILE D  46 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ILE D  51 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 71
    Processing helix  chain 'D' and resid 84 through 139
      removed outlier: 4.065A  pdb=" N   MET D  89 " --> pdb=" O   PRO D  85 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   VAL D  90 " --> pdb=" O   PHE D  86 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LYS D 102 " --> pdb=" O   THR D  98 " (cutoff:3.500A)
      Proline residue:  D 129  - end of helix
    Processing helix  chain 'D' and resid 142 through 169
    Processing helix  chain 'D' and resid 170 through 175
      removed outlier: 5.630A  pdb=" N   GLU D 173 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 194
      removed outlier: 4.202A  pdb=" N   LEU D 186 " --> pdb=" O   GLN D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 202
    Processing helix  chain 'D' and resid 217 through 235
    Processing helix  chain 'D' and resid 264 through 268
    Processing helix  chain 'D' and resid 281 through 285
    Processing helix  chain 'D' and resid 289 through 300
      removed outlier: 4.331A  pdb=" N   TYR D 293 " --> pdb=" O   GLY D 289 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 324 through 327
    Processing helix  chain 'D' and resid 328 through 334
    Processing helix  chain 'E' and resid 2 through 9
    Processing helix  chain 'E' and resid 11 through 30
      removed outlier: 3.546A  pdb=" N   PHE E  16 " --> pdb=" O   TRP E  12 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU E  17 " --> pdb=" O   ILE E  13 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLN E  19 " --> pdb=" O   ALA E  15 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLN E  20 " --> pdb=" O   PHE E  16 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA E  21 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   PHE E  28 " --> pdb=" O   LEU E  24 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL E  29 " --> pdb=" O   PHE E  25 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASP E  30 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 61
      removed outlier: 3.951A  pdb=" N   ARG E  58 " --> pdb=" O   TRP E  54 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LYS E  59 " --> pdb=" O   PHE E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 71
    Processing helix  chain 'E' and resid 84 through 138
      Proline residue:  E 129  - end of helix
    Processing helix  chain 'E' and resid 143 through 170
    Processing helix  chain 'E' and resid 171 through 175
    Processing helix  chain 'E' and resid 183 through 194
    Processing helix  chain 'E' and resid 194 through 202
    Processing helix  chain 'E' and resid 217 through 235
      removed outlier: 3.919A  pdb=" N   LEU E 221 " --> pdb=" O   ASP E 217 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 281 through 287
    Processing helix  chain 'E' and resid 289 through 303
      removed outlier: 4.064A  pdb=" N   TYR E 293 " --> pdb=" O   GLY E 289 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA E 300 " --> pdb=" O   LYS E 296 " (cutoff:3.500A)
      Proline residue:  E 301  - end of helix
    Processing helix  chain 'E' and resid 324 through 327
    Processing helix  chain 'E' and resid 328 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 330
      removed outlier: 3.640A  pdb=" N   LEU A 511 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 353 through 354
      removed outlier: 4.002A  pdb=" N   LYS A 354 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY A 485 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 426
      removed outlier: 3.640A  pdb=" N   LYS A 425 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   MET A 383 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 9.136A  pdb=" N   VAL A 458 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
      removed outlier: 7.116A  pdb=" N   ALA A 386 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 457 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A 404 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   PHE A 405 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   LEU A 440 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 30
    Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 14
    Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90
      removed outlier: 7.515A  pdb=" N   GLY B  88 " --> pdb=" O   PHE B 166 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   ASP B 168 " --> pdb=" O   GLY B  88 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   ILE B  90 " --> pdb=" O   ASP B 168 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ILE B 165 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   VAL B 200 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ALA B 167 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   PHE B  35 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE B 214 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER B  37 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 88
      removed outlier: 5.809A  pdb=" N   GLY C  88 " --> pdb=" O   PHE C 166 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ILE C 198 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA C 167 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET C 199 " --> pdb=" O   VAL C  36 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 66
    Processing sheet with id=AA9, first strand: chain 'D' and resid 205 through 209
      removed outlier: 3.564A  pdb=" N   LYS D 248 " --> pdb=" O   GLN D 251 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN D 251 " --> pdb=" O   LYS D 248 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 305 through 311
    Processing sheet with id=AB2, first strand: chain 'E' and resid 179 through 182
      removed outlier: 4.006A  pdb=" N   GLU E 179 " --> pdb=" O   SER E 216 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   SER E 216 " --> pdb=" O   GLU E 179 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL E 214 " --> pdb=" O   ILE E 181 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 205 through 209
      removed outlier: 5.819A  pdb=" N   ASP E 206 " --> pdb=" O   ILE E 243 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   SER E 245 " --> pdb=" O   ASP E 206 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   GLN E 208 " --> pdb=" O   SER E 245 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   GLN E 247 " --> pdb=" O   GLN E 208 " (cutoff:3.500A)

    773 hydrogen bonds defined for protein.
    2229 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2344
        1.31 -     1.44: 3764
        1.44 -     1.56: 8465
        1.56 -     1.69: 22
        1.69 -     1.81: 114
  Bond restraints: 14709
  Sorted by residual:
  bond pdb=" C10 OLA E 401 "
       pdb=" C9  OLA E 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.470 -0.138 2.00e-02 2.50e+03 4.75e+01
  bond pdb=" C16 6OU A 702 "
       pdb=" O18 6OU A 702 "
    ideal  model  delta    sigma   weight residual
    1.327  1.455 -0.128 2.00e-02 2.50e+03 4.08e+01
  bond pdb=" C16 6OU A 703 "
       pdb=" O18 6OU A 703 "
    ideal  model  delta    sigma   weight residual
    1.327  1.454 -0.127 2.00e-02 2.50e+03 4.02e+01
  bond pdb=" C14 6OU A 702 "
       pdb=" C15 6OU A 702 "
    ideal  model  delta    sigma   weight residual
    1.521  1.607 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C31 6OU A 703 "
       pdb=" O30 6OU A 703 "
    ideal  model  delta    sigma   weight residual
    1.331  1.417 -0.086 2.00e-02 2.50e+03 1.84e+01
  ... (remaining 14704 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.18: 19726
        5.18 -    10.36: 45
       10.36 -    15.54: 3
       15.54 -    20.72: 2
       20.72 -    25.90: 2
  Bond angle restraints: 19778
  Sorted by residual:
  angle pdb=" C40 6OU A 702 "
        pdb=" C41 6OU A 702 "
        pdb=" C42 6OU A 702 "
      ideal   model   delta    sigma   weight residual
     127.56  153.46  -25.90 3.00e+00 1.11e-01 7.45e+01
  angle pdb=" C40 6OU A 703 "
        pdb=" C41 6OU A 703 "
        pdb=" C42 6OU A 703 "
      ideal   model   delta    sigma   weight residual
     127.56  151.55  -23.99 3.00e+00 1.11e-01 6.40e+01
  angle pdb=" O22 6OU A 702 "
        pdb=" P23 6OU A 702 "
        pdb=" O26 6OU A 702 "
      ideal   model   delta    sigma   weight residual
      93.95  110.61  -16.66 3.00e+00 1.11e-01 3.08e+01
  angle pdb=" C39 6OU A 703 "
        pdb=" C40 6OU A 703 "
        pdb=" C41 6OU A 703 "
      ideal   model   delta    sigma   weight residual
     127.60  111.71   15.89 3.00e+00 1.11e-01 2.81e+01
  angle pdb=" O22 6OU A 703 "
        pdb=" P23 6OU A 703 "
        pdb=" O26 6OU A 703 "
      ideal   model   delta    sigma   weight residual
      93.95  108.87  -14.92 3.00e+00 1.11e-01 2.47e+01
  ... (remaining 19773 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.32: 8352
       27.32 -    54.63: 468
       54.63 -    81.95: 50
       81.95 -   109.27: 6
      109.27 -   136.58: 3
  Dihedral angle restraints: 8879
    sinusoidal: 3667
      harmonic: 5212
  Sorted by residual:
  dihedral pdb=" C07 6OU A 702 "
           pdb=" C08 6OU A 702 "
           pdb=" C09 6OU A 702 "
           pdb=" C10 6OU A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.90   43.32  136.58     1      3.00e+01 1.11e-03 1.84e+01
  dihedral pdb=" C08 6OU A 703 "
           pdb=" C09 6OU A 703 "
           pdb=" C10 6OU A 703 "
           pdb=" C11 6OU A 703 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.07   44.95  135.12     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" CA  LYS A 265 "
           pdb=" C   LYS A 265 "
           pdb=" N   SER A 266 "
           pdb=" CA  SER A 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.12   20.88     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 8876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1880
       0.060 -    0.120: 335
       0.120 -    0.180: 28
       0.180 -    0.240: 2
       0.240 -    0.300: 1
  Chirality restraints: 2246
  Sorted by residual:
  chirality pdb=" C20 6OU A 702 "
            pdb=" C19 6OU A 702 "
            pdb=" C21 6OU A 702 "
            pdb=" O30 6OU A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.65   -0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CB  ILE C 198 "
            pdb=" CA  ILE C 198 "
            pdb=" CG1 ILE C 198 "
            pdb=" CG2 ILE C 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE A 563 "
            pdb=" N   ILE A 563 "
            pdb=" C   ILE A 563 "
            pdb=" CB  ILE A 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.78e-01
  ... (remaining 2243 not shown)

  Planarity restraints: 2468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA E 401 "    0.287 2.00e-02 2.50e+03   2.20e-01 4.82e+02
        pdb=" C11 OLA E 401 "   -0.112 2.00e-02 2.50e+03
        pdb=" C8  OLA E 401 "    0.116 2.00e-02 2.50e+03
        pdb=" C9  OLA E 401 "   -0.291 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 153 "    0.031 2.00e-02 2.50e+03   2.44e-02 1.49e+01
        pdb=" CG  TRP D 153 "   -0.065 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 153 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 153 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 153 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 153 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 153 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 153 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 153 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 153 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 197 "   -0.008 2.00e-02 2.50e+03   1.56e-02 6.06e+00
        pdb=" CG  TRP D 197 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 197 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 197 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 197 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 197 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 197 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 197 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 197 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2465 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 982
        2.73 -     3.27: 14476
        3.27 -     3.82: 22689
        3.82 -     4.36: 25463
        4.36 -     4.90: 44529
  Nonbonded interactions: 108139
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 362 "
            pdb=" OD1 ASN A 382 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" NH2 ARG D   9 "
            pdb=" OE2 GLU D  60 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" OG  SER C 145 "
            pdb=" OE1 GLN C 148 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER A 406 "
            pdb=" O   ALA A 457 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG1 THR A 451 "
            pdb=" O   MET A 455 "
     model   vdw
     2.268 3.040
  ... (remaining 108134 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'E' and resid 1 through 334)
}

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:             3.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.700
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
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   0.138  14709  Z= 0.284
  Angle     :  0.805  25.896  19778  Z= 0.387
  Chirality :  0.045   0.300   2246
  Planarity :  0.006   0.220   2468
  Dihedral  : 15.950 136.583   5505
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  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: -0.13 (0.21), residues: 1779
  helix:  0.99 (0.17), residues: 1003
  sheet: -1.02 (0.45), residues: 169
  loop : -1.60 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 226 
 TYR   0.023   0.002   TYR A 315 
 PHE   0.026   0.002   PHE A 529 
 TRP   0.065   0.004   TRP D 153 
 HIS   0.008   0.001   HIS A 596 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00622 /  0.28 (14709)
  covalent geometry    : angle       0.80502 /  0.39 (19778)
  hydrogen bonds       : bond        0.15498 /  9.96 (  773)
  hydrogen bonds       : angle       5.71354 /  4.01 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   57 TYR cc_start: 0.8347 (t80) cc_final: 0.8086 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1068
  time to fit residues: 26.2681
Evaluate side-chains
  144 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.4980
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 503 GLN
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 165 HIS ** 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 = 0.4507 r_free = 0.4507 target = 0.228662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.195076 restraints weight = 19040.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.191086 restraints weight = 36070.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.183974 restraints weight = 38534.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.180705 restraints weight = 42188.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.177617 restraints weight = 35895.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14709  Z= 0.134
  Angle     :  0.571  12.582  19778  Z= 0.291
  Chirality :  0.042   0.265   2246
  Planarity :  0.003   0.037   2468
  Dihedral  :  9.256 107.384   1996
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.55 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  7.10 %
    Favored  : 92.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.17 (0.21), residues: 1779
  helix:  1.27 (0.17), residues: 1006
  sheet: -0.95 (0.45), residues: 165
  loop : -1.54 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 226 
 TYR   0.033   0.002   TYR E 151 
 PHE   0.020   0.001   PHE A 529 
 TRP   0.019   0.002   TRP D 153 
 HIS   0.008   0.001   HIS D 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 (14709)
  covalent geometry    : angle       0.57138 /  0.29 (19778)
  hydrogen bonds       : bond        0.06099 /  3.92 (  773)
  hydrogen bonds       : angle       4.58974 /  3.24 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 149
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.5666 (mtt) cc_final: 0.5359 (mtm)
REVERT: B   83 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7830 (ttm170)
REVERT: D   41 MET cc_start: 0.5566 (mmp) cc_final: 0.5350 (mmp)
  outliers start: 8
  outliers final: 7
  residues processed: 151
  average time/residue: 0.0981
  time to fit residues: 22.1983
Evaluate side-chains
  146 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  290 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 122 optimal weight:    4.9990
   chunk 162 optimal weight:    0.8980
   chunk 140 optimal weight:    6.9990
   chunk 115 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 151 optimal weight:    3.9990
   overall best weight:    1.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.225094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.185883 restraints weight = 18689.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.182647 restraints weight = 37290.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.177815 restraints weight = 35040.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.173142 restraints weight = 36658.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.170375 restraints weight = 34016.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14709  Z= 0.201
  Angle     :  0.613  13.143  19778  Z= 0.311
  Chirality :  0.044   0.241   2246
  Planarity :  0.003   0.040   2468
  Dihedral  :  8.954  98.221   1996
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.34 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.68 %
    Favored  : 88.36 %
  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:  0.04 (0.21), residues: 1779
  helix:  1.16 (0.17), residues: 1004
  sheet: -1.03 (0.43), residues: 167
  loop : -1.57 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 107 
 TYR   0.028   0.002   TYR E 151 
 PHE   0.029   0.002   PHE A 529 
 TRP   0.016   0.002   TRP E 122 
 HIS   0.006   0.001   HIS A 596 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00489 /  0.20 (14709)
  covalent geometry    : angle       0.61294 /  0.31 (19778)
  hydrogen bonds       : bond        0.07149 /  4.61 (  773)
  hydrogen bonds       : angle       4.53816 /  3.21 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7489 (ttm170)
  outliers start: 15
  outliers final: 11
  residues processed: 149
  average time/residue: 0.1047
  time to fit residues: 22.8521
Evaluate side-chains
  148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue  130 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0770
   chunk 4 optimal weight:    0.6980
   chunk 167 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 510 HIS
D 124 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.227737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.190390 restraints weight = 18714.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.187231 restraints weight = 37414.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.182246 restraints weight = 33927.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.179363 restraints weight = 35623.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.174677 restraints weight = 35075.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  14709  Z= 0.127
  Angle     :  0.541  11.741  19778  Z= 0.272
  Chirality :  0.041   0.221   2246
  Planarity :  0.003   0.037   2468
  Dihedral  :  8.315  85.227   1996
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.78 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.96 %
    Favored  : 86.63 %
  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:  0.28 (0.21), residues: 1779
  helix:  1.39 (0.17), residues: 1014
  sheet: -1.06 (0.41), residues: 176
  loop : -1.53 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 107 
 TYR   0.024   0.001   TYR E 151 
 PHE   0.021   0.001   PHE A 529 
 TRP   0.015   0.002   TRP D 122 
 HIS   0.004   0.001   HIS D 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 (14709)
  covalent geometry    : angle       0.54143 /  0.27 (19778)
  hydrogen bonds       : bond        0.05808 /  3.75 (  773)
  hydrogen bonds       : angle       4.23642 /  3.00 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   83 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7850 (ttm170)
  outliers start: 22
  outliers final: 15
  residues processed: 163
  average time/residue: 0.1048
  time to fit residues: 25.3531
Evaluate side-chains
  153 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  290 MET
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 101 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 137 optimal weight:    6.9990
   chunk 161 optimal weight:    0.4980
   chunk 104 optimal weight:    0.1980
   chunk 162 optimal weight:   50.0000
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS
** B  20 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 = 0.4484 r_free = 0.4484 target = 0.226074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.189469 restraints weight = 18748.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.186231 restraints weight = 35235.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.183315 restraints weight = 36195.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.179871 restraints weight = 37065.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.175341 restraints weight = 38447.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14709  Z= 0.167
  Angle     :  0.580  10.215  19778  Z= 0.294
  Chirality :  0.042   0.164   2246
  Planarity :  0.003   0.039   2468
  Dihedral  :  8.257  82.412   1996
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.44 %
    Favored  : 84.90 %
  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:  0.23 (0.21), residues: 1779
  helix:  1.33 (0.17), residues: 1008
  sheet: -1.00 (0.41), residues: 163
  loop : -1.51 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 107 
 TYR   0.022   0.002   TYR E 151 
 PHE   0.028   0.001   PHE A 529 
 TRP   0.017   0.002   TRP E 122 
 HIS   0.004   0.001   HIS A 596 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 (14709)
  covalent geometry    : angle       0.57995 /  0.29 (19778)
  hydrogen bonds       : bond        0.06408 /  4.14 (  773)
  hydrogen bonds       : angle       4.23775 /  3.00 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 TYR cc_start: 0.6423 (m-10) cc_final: 0.6169 (m-80)
REVERT: B   83 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7799 (ttm170)
  outliers start: 26
  outliers final: 19
  residues processed: 152
  average time/residue: 0.1108
  time to fit residues: 25.5499
Evaluate side-chains
  154 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain E residue  130 LEU
Chi-restraints excluded: chain E residue  290 MET
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 77 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 41 optimal weight:   30.0000
   chunk 89 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS
** B  20 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 = 0.4481 r_free = 0.4481 target = 0.225758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.189996 restraints weight = 18783.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.187426 restraints weight = 34895.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.183341 restraints weight = 31990.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.179248 restraints weight = 29391.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.176190 restraints weight = 36111.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14709  Z= 0.166
  Angle     :  0.574   9.545  19778  Z= 0.290
  Chirality :  0.042   0.167   2246
  Planarity :  0.003   0.039   2468
  Dihedral  :  8.214  81.539   1996
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.17 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.82 %
    Favored  : 84.01 %
  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:  0.28 (0.21), residues: 1779
  helix:  1.35 (0.17), residues: 1008
  sheet: -0.90 (0.41), residues: 158
  loop : -1.47 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 107 
 TYR   0.019   0.002   TYR E 151 
 PHE   0.026   0.001   PHE A 529 
 TRP   0.022   0.002   TRP D 122 
 HIS   0.012   0.001   HIS D 124 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.17 (14709)
  covalent geometry    : angle       0.57384 /  0.29 (19778)
  hydrogen bonds       : bond        0.06397 /  4.09 (  773)
  hydrogen bonds       : angle       4.16116 /  2.95 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7060 (mt0)
REVERT: A  315 TYR cc_start: 0.6538 (m-10) cc_final: 0.6327 (m-80)
REVERT: B   83 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7843 (ttp-170)
REVERT: C   71 MET cc_start: 0.3406 (ppp) cc_final: 0.3081 (ppp)
REVERT: C   74 MET cc_start: -0.0604 (pmm) cc_final: -0.3117 (tmm)
  outliers start: 34
  outliers final: 20
  residues processed: 160
  average time/residue: 0.1133
  time to fit residues: 27.2671
Evaluate side-chains
  156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   91 GLN
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 124 optimal weight:    5.9990
   chunk 83 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 125 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 503 GLN
A 510 HIS
** B  20 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 = 0.4499 r_free = 0.4499 target = 0.228070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.193534 restraints weight = 19089.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.190085 restraints weight = 32886.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.185410 restraints weight = 28409.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.183576 restraints weight = 33346.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.181843 restraints weight = 27030.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14709  Z= 0.123
  Angle     :  0.535   9.005  19778  Z= 0.271
  Chirality :  0.041   0.189   2246
  Planarity :  0.003   0.039   2468
  Dihedral  :  7.892  75.721   1996
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.80 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.49 (0.21), residues: 1779
  helix:  1.51 (0.17), residues: 1009
  sheet: -0.83 (0.41), residues: 165
  loop : -1.38 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 107 
 TYR   0.019   0.001   TYR E 151 
 PHE   0.021   0.001   PHE A 529 
 TRP   0.025   0.002   TRP E 122 
 HIS   0.004   0.001   HIS D 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 (14709)
  covalent geometry    : angle       0.53480 /  0.27 (19778)
  hydrogen bonds       : bond        0.05529 /  3.56 (  773)
  hydrogen bonds       : angle       3.97564 /  2.82 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 16
  residues processed: 154
  average time/residue: 0.0966
  time to fit residues: 22.7945
Evaluate side-chains
  149 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 141 optimal weight:   50.0000
   chunk 12 optimal weight:    0.0020
   chunk 112 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 78 optimal weight:    0.5980
   chunk 130 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS
B  20 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.228858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.195825 restraints weight = 18978.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.191296 restraints weight = 40239.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.186529 restraints weight = 37462.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.183315 restraints weight = 39626.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.180261 restraints weight = 34602.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088  14709  Z= 0.117
  Angle     :  0.542  11.558  19778  Z= 0.271
  Chirality :  0.041   0.276   2246
  Planarity :  0.003   0.037   2468
  Dihedral  :  7.629  72.074   1996
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.31 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.54 (0.21), residues: 1779
  helix:  1.55 (0.17), residues: 1023
  sheet: -0.79 (0.41), residues: 165
  loop : -1.43 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 107 
 TYR   0.017   0.001   TYR E 151 
 PHE   0.036   0.001   PHE C  35 
 TRP   0.028   0.002   TRP E 122 
 HIS   0.003   0.001   HIS B  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 (14709)
  covalent geometry    : angle       0.54181 /  0.27 (19778)
  hydrogen bonds       : bond        0.05178 /  3.33 (  773)
  hydrogen bonds       : angle       3.90755 /  2.77 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   74 MET cc_start: -0.0774 (pmm) cc_final: -0.3216 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 147
  average time/residue: 0.1170
  time to fit residues: 26.3907
Evaluate side-chains
  148 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 129 optimal weight:    0.5980
   chunk 117 optimal weight:    0.8980
   chunk 156 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0770
   chunk 106 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.228574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.196021 restraints weight = 19222.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.191647 restraints weight = 39130.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.186112 restraints weight = 36154.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.183334 restraints weight = 38930.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180326 restraints weight = 34639.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.4031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14709  Z= 0.123
  Angle     :  0.554  10.773  19778  Z= 0.276
  Chirality :  0.041   0.268   2246
  Planarity :  0.003   0.036   2468
  Dihedral  :  7.544  71.789   1996
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.76 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.56 (0.21), residues: 1779
  helix:  1.55 (0.17), residues: 1023
  sheet: -0.68 (0.42), residues: 151
  loop : -1.42 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 107 
 TYR   0.018   0.001   TYR E 151 
 PHE   0.033   0.001   PHE C  35 
 TRP   0.034   0.002   TRP E 122 
 HIS   0.016   0.001   HIS A 510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (14709)
  covalent geometry    : angle       0.55352 /  0.28 (19778)
  hydrogen bonds       : bond        0.05282 /  3.41 (  773)
  hydrogen bonds       : angle       3.88099 /  2.75 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   74 MET cc_start: -0.0695 (pmm) cc_final: -0.3189 (tmm)
REVERT: E   92 ARG cc_start: 0.7357 (mmm160) cc_final: 0.7127 (mmm160)
  outliers start: 24
  outliers final: 20
  residues processed: 149
  average time/residue: 0.1134
  time to fit residues: 26.1074
Evaluate side-chains
  150 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0070
   chunk 160 optimal weight:    0.9980
   chunk 144 optimal weight:    0.8980
   chunk 117 optimal weight:    0.1980
   chunk 14 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 65 optimal weight:   20.0000
   chunk 159 optimal weight:    6.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.229121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.194561 restraints weight = 18613.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.190674 restraints weight = 34406.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.186699 restraints weight = 32862.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.182174 restraints weight = 31203.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.177239 restraints weight = 36434.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  14709  Z= 0.121
  Angle     :  0.552  13.363  19778  Z= 0.276
  Chirality :  0.041   0.322   2246
  Planarity :  0.003   0.034   2468
  Dihedral  :  7.316  69.437   1996
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.15 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.65 (0.21), residues: 1779
  helix:  1.62 (0.17), residues: 1022
  sheet: -0.64 (0.43), residues: 151
  loop : -1.35 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 107 
 TYR   0.016   0.001   TYR E 151 
 PHE   0.032   0.001   PHE C  35 
 TRP   0.034   0.002   TRP E 122 
 HIS   0.003   0.001   HIS D 134 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 (14709)
  covalent geometry    : angle       0.55248 /  0.28 (19778)
  hydrogen bonds       : bond        0.05094 /  3.28 (  773)
  hydrogen bonds       : angle       3.82572 /  2.70 ( 2229)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  315 TYR cc_start: 0.6214 (m-80) cc_final: 0.5990 (m-80)
REVERT: A  505 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6226 (p0)
REVERT: C   74 MET cc_start: -0.0473 (pmm) cc_final: -0.3014 (tmm)
REVERT: E   92 ARG cc_start: 0.7329 (mmm160) cc_final: 0.7101 (mmm160)
  outliers start: 22
  outliers final: 20
  residues processed: 150
  average time/residue: 0.1185
  time to fit residues: 27.0848
Evaluate side-chains
  152 residues out of total 1563 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   95 MET
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  300 SER
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  510 HIS
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain B residue   52 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue   86 HIS
Chi-restraints excluded: chain C residue   94 TYR
Chi-restraints excluded: chain C residue  136 LEU
Chi-restraints excluded: chain D residue   30 ASP
Chi-restraints excluded: chain D residue  113 GLU
Chi-restraints excluded: chain E residue   23 MET
Chi-restraints excluded: chain E residue  308 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 177
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 135 optimal weight:   30.0000
   chunk 168 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 159 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 172 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    2.0586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  61 HIS
D  37 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.223996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.186101 restraints weight = 18637.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.183145 restraints weight = 31367.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.178488 restraints weight = 26763.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.174250 restraints weight = 31278.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.172545 restraints weight = 36735.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087  14709  Z= 0.238
  Angle     :  0.687  15.632  19778  Z= 0.342
  Chirality :  0.045   0.273   2246
  Planarity :  0.004   0.039   2468
  Dihedral  :  8.127  83.196   1996
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 17.40 %
    Favored  : 81.38 %
  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:  0.16 (0.21), residues: 1779
  helix:  1.15 (0.17), residues: 1022
  sheet: -0.70 (0.40), residues: 160
  loop : -1.45 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 107 
 TYR   0.025   0.002   TYR A 311 
 PHE   0.034   0.002   PHE A 529 
 TRP   0.035   0.002   TRP E 122 
 HIS   0.014   0.001   HIS A 510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00586 /  0.24 (14709)
  covalent geometry    : angle       0.68669 /  0.34 (19778)
  hydrogen bonds       : bond        0.07304 /  4.71 (  773)
  hydrogen bonds       : angle       4.14934 /  2.94 ( 2229)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2084.54 seconds
wall clock time: 37 minutes 3.17 seconds (2223.17 seconds total)