Starting phenix.real_space_refine
on Wed Mar  4 02:32:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sz9_10350/03_2026/6sz9_10350.map"
  }
  resolution = 3.7
  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=  -0.000 sd=   0.841
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
     Zn      1      6.06       5
     S      48      5.16       5
     C    6520      2.51       5
     N    1748      2.21       5
     O    1916      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10233
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3665
          Classifications: {'peptide': 473}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 19, 'TRANS': 453}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 2085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 2085
          Classifications: {'peptide': 259}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
    Chain: "C"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1615
          Classifications: {'peptide': 202}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 197}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 2284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2284
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 583
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 583
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 3, 'TRANS': 69}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6091  SG  CYS C  46      72.511  31.236  60.268  1.00 35.96           S
  ATOM   6117  SG  CYS C  49      75.680  32.328  60.598  1.00 29.67           S
  ATOM   6346  SG  CYS C  78      73.743  35.280  59.358  1.00 29.81           S
  ATOM   6369  SG  CYS C  81      74.403  32.503  57.235  1.00 27.56           S

  Time building chain proxies: 2.14, per 1000 atoms: 0.21
  Number of scatterers: 10233
  At special positions: 0
  Unit cell: (119.13, 110.77, 122.265, 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)
     Zn      1     29.99
     S      48     16.00
     O    1916      8.00
     N    1748      7.00
     C    6520      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: 0.67
  Conformation dependent library (CDL) restraints added in 457.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 301 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  46 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  81 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  49 "
        pdb="ZN    ZN C 301 " - pdb=" SG  CYS C  78 "
      Number of angles added : 6


  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2444

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      59.5% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.702A  pdb=" N   THR A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 152
      removed outlier: 3.701A  pdb=" N   THR A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 178
    Processing helix  chain 'A' and resid 218 through 228
    Processing helix  chain 'A' and resid 240 through 262
      removed outlier: 3.939A  pdb=" N   GLU A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 3.833A  pdb=" N   ILE A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
    Processing helix  chain 'A' and resid 303 through 316
      removed outlier: 4.063A  pdb=" N   THR A 307 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      Proline residue:  A 309  - end of helix
    Processing helix  chain 'A' and resid 325 through 353
      removed outlier: 4.123A  pdb=" N   SER A 330 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   GLU A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   GLN A 335 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   GLN A 342 " --> pdb=" O   PHE A 338 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   LEU A 343 " --> pdb=" O   ILE A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 374
      removed outlier: 3.537A  pdb=" N   VAL A 371 " --> pdb=" O   PHE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 408
      removed outlier: 4.264A  pdb=" N   LEU A 391 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER A 392 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ASN A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 459
      removed outlier: 3.714A  pdb=" N   GLY A 459 " --> pdb=" O   ARG A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 476
    Processing helix  chain 'A' and resid 479 through 487
    Processing helix  chain 'A' and resid 594 through 615
      removed outlier: 3.677A  pdb=" N   MET A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   LYS A 600 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   SER A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   GLY A 615 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 638
      removed outlier: 3.795A  pdb=" N   SER A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 658
    Processing helix  chain 'B' and resid 126 through 134
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.664A  pdb=" N   ILE B 141 " --> pdb=" O   TRP B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 172
    Processing helix  chain 'B' and resid 196 through 207
      removed outlier: 4.057A  pdb=" N   ARG B 202 " --> pdb=" O   GLY B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 234
      removed outlier: 3.550A  pdb=" N   ASN B 234 " --> pdb=" O   MET B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 253
      removed outlier: 3.729A  pdb=" N   ALA B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 260
      No H-bonds generated for 'chain 'B' and resid 258 through 260'
    Processing helix  chain 'B' and resid 261 through 266
      removed outlier: 3.637A  pdb=" N   MET B 265 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 280
    Processing helix  chain 'B' and resid 283 through 296
    Processing helix  chain 'B' and resid 297 through 299
      No H-bonds generated for 'chain 'B' and resid 297 through 299'
    Processing helix  chain 'B' and resid 302 through 306
      removed outlier: 3.858A  pdb=" N   GLU B 305 " --> pdb=" O   PRO B 302 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   PHE B 306 " --> pdb=" O   SER B 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 302 through 306'
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.998A  pdb=" N   VAL B 312 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 323
      removed outlier: 3.532A  pdb=" N   VAL B 323 " --> pdb=" O   MET B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 346
      removed outlier: 3.755A  pdb=" N   MET B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 346 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 366
      removed outlier: 4.311A  pdb=" N   ARG B 359 " --> pdb=" O   ASP B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 376
    Processing helix  chain 'C' and resid 18 through 28
      removed outlier: 3.789A  pdb=" N   ILE C  27 " --> pdb=" O   SER C  23 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASP C  28 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 43
      removed outlier: 3.530A  pdb=" N   LYS C  32 " --> pdb=" O   ASP C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 84
    Processing helix  chain 'C' and resid 107 through 123
    Processing helix  chain 'C' and resid 128 through 151
      removed outlier: 3.620A  pdb=" N   ALA C 132 " --> pdb=" O   TYR C 128 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER C 138 " --> pdb=" O   ASN C 134 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLU C 147 " --> pdb=" O   SER C 143 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLU C 148 " --> pdb=" O   GLN C 144 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LYS C 149 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 166
    Processing helix  chain 'C' and resid 171 through 179
    Processing helix  chain 'C' and resid 191 through 207
      removed outlier: 3.523A  pdb=" N   ALA C 207 " --> pdb=" O   LEU C 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 29
    Processing helix  chain 'D' and resid 36 through 42
    Processing helix  chain 'D' and resid 48 through 85
      removed outlier: 4.499A  pdb=" N   ILE D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
      Proline residue:  D  56  - end of helix
      removed outlier: 3.754A  pdb=" N   ASN D  59 " --> pdb=" O   ILE D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 159
      removed outlier: 4.106A  pdb=" N   GLU D 102 " --> pdb=" O   ALA D  98 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER D 103 " --> pdb=" O   GLY D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 181
      removed outlier: 3.620A  pdb=" N   CYS D 181 " --> pdb=" O   ALA D 177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 203
      removed outlier: 4.101A  pdb=" N   LYS D 192 " --> pdb=" O   SER D 188 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   TYR D 193 " --> pdb=" O   GLN D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 266
      removed outlier: 5.421A  pdb=" N   GLU D 221 " --> pdb=" O   THR D 217 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   LEU D 222 " --> pdb=" O   ASN D 218 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR D 231 " --> pdb=" O   GLU D 227 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS D 232 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   HIS D 242 " --> pdb=" O   ASP D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 276 through 283
    Processing helix  chain 'E' and resid 8 through 19
      removed outlier: 3.713A  pdb=" N   GLY E  19 " --> pdb=" O   ALA E  15 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 22 through 39
      removed outlier: 3.602A  pdb=" N   ALA E  26 " --> pdb=" O   SER E  22 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 64
    Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120
      removed outlier: 3.924A  pdb=" N   GLY A 109 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   PHE A 120 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   PHE A 107 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ALA A 558 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE A 464 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 466 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189
      removed outlier: 6.407A  pdb=" N   LEU A 186 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   LEU A 380 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE A 188 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   TYR A 159 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289
      removed outlier: 3.715A  pdb=" N   VAL A 297 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 176
    Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 60
    Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 101

    521 hydrogen bonds defined for protein.
    1542 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: 1.75

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3327
        1.34 -     1.46: 1857
        1.46 -     1.58: 5151
        1.58 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10415
  Sorted by residual:
  bond pdb=" N   PHE C  48 "
       pdb=" CA  PHE C  48 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.25e+00
  bond pdb=" N   CYS C  78 "
       pdb=" CA  CYS C  78 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.033 1.31e-02 5.83e+03 6.20e+00
  bond pdb=" N   CYS C  49 "
       pdb=" CA  CYS C  49 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.50e-02 4.44e+03 5.57e+00
  bond pdb=" N   GLN C  47 "
       pdb=" CA  GLN C  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.57e+00
  bond pdb=" N   GLY C  50 "
       pdb=" CA  GLY C  50 "
    ideal  model  delta    sigma   weight residual
    1.446  1.479 -0.032 1.50e-02 4.44e+03 4.68e+00
  ... (remaining 10410 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 13527
        1.90 -     3.80: 469
        3.80 -     5.71: 39
        5.71 -     7.61: 16
        7.61 -     9.51: 7
  Bond angle restraints: 14058
  Sorted by residual:
  angle pdb=" C   ASP A 286 "
        pdb=" N   LYS A 287 "
        pdb=" CA  LYS A 287 "
      ideal   model   delta    sigma   weight residual
     122.07  127.34   -5.27 1.43e+00 4.89e-01 1.36e+01
  angle pdb=" C   TYR D  29 "
        pdb=" N   ASN D  30 "
        pdb=" CA  ASN D  30 "
      ideal   model   delta    sigma   weight residual
     122.40  127.55   -5.15 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" N   ASP A 308 "
        pdb=" CA  ASP A 308 "
        pdb=" C   ASP A 308 "
      ideal   model   delta    sigma   weight residual
     109.81  116.73   -6.92 2.21e+00 2.05e-01 9.81e+00
  angle pdb=" CA  LYS A 287 "
        pdb=" CB  LYS A 287 "
        pdb=" CG  LYS A 287 "
      ideal   model   delta    sigma   weight residual
     114.10  120.31   -6.21 2.00e+00 2.50e-01 9.65e+00
  angle pdb=" CA  CYS C  79 "
        pdb=" C   CYS C  79 "
        pdb=" O   CYS C  79 "
      ideal   model   delta    sigma   weight residual
     120.55  117.34    3.21 1.06e+00 8.90e-01 9.15e+00
  ... (remaining 14053 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5605
       17.86 -    35.71: 642
       35.71 -    53.56: 100
       53.56 -    71.42: 24
       71.42 -    89.27: 11
  Dihedral angle restraints: 6382
    sinusoidal: 2612
      harmonic: 3770
  Sorted by residual:
  dihedral pdb=" CA  GLU A 591 "
           pdb=" C   GLU A 591 "
           pdb=" N   PRO A 592 "
           pdb=" CA  PRO A 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  LYS A 474 "
           pdb=" C   LYS A 474 "
           pdb=" N   ALA A 475 "
           pdb=" CA  ALA A 475 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.42  -19.58     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ASP A 366 "
           pdb=" C   ASP A 366 "
           pdb=" N   PHE A 367 "
           pdb=" CA  PHE A 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.81  -19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 6379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1244
       0.056 -    0.111: 280
       0.111 -    0.167: 45
       0.167 -    0.223: 9
       0.223 -    0.278: 3
  Chirality restraints: 1581
  Sorted by residual:
  chirality pdb=" CB  VAL A 332 "
            pdb=" CA  VAL A 332 "
            pdb=" CG1 VAL A 332 "
            pdb=" CG2 VAL A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CB  ILE A 131 "
            pdb=" CA  ILE A 131 "
            pdb=" CG1 ILE A 131 "
            pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  ILE D  44 "
            pdb=" CA  ILE D  44 "
            pdb=" CG1 ILE D  44 "
            pdb=" CG2 ILE D  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 1578 not shown)

  Planarity restraints: 1809
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  44 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.84e+00
        pdb=" N   PRO D  45 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO D  45 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  45 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 289 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.64e+00
        pdb=" N   PRO A 290 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 362 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.50e+00
        pdb=" C   GLU B 362 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 362 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE B 363 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1806 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2983
        2.81 -     3.34: 9194
        3.34 -     3.86: 16595
        3.86 -     4.38: 18277
        4.38 -     4.90: 31998
  Nonbonded interactions: 79047
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 114 "
            pdb=" OE1 GLU A 116 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   ALA A 150 "
            pdb=" OG  SER A 155 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ILE A 483 "
            pdb=" OG1 THR A 487 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ASP D  82 "
            pdb=" OH  TYR D 271 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OD1 ASN C 124 "
            pdb=" OG1 THR D  21 "
     model   vdw
     2.319 3.040
  ... (remaining 79042 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.450
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.160  10419  Z= 0.237
  Angle     :  0.868  26.533  14064  Z= 0.462
  Chirality :  0.050   0.278   1581
  Planarity :  0.006   0.060   1809
  Dihedral  : 15.573  89.271   3938
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  9.90 %
    Favored  : 89.83 %
  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: -3.82 (0.18), residues: 1274
  helix: -2.19 (0.15), residues: 717
  sheet: -2.04 (0.69), residues: 54
  loop : -2.96 (0.22), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 296 
 TYR   0.025   0.002   TYR A 440 
 PHE   0.027   0.002   PHE D 254 
 TRP   0.010   0.001   TRP B 159 
 HIS   0.005   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (10415)
  covalent geometry    : angle       0.81718 (14058)
  hydrogen bonds       : bond        0.11761 (  521)
  hydrogen bonds       : angle       6.15066 ( 1542)
  metal coordination   : bond        0.11764 (    4)
  metal coordination   : angle      14.13546 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 MET cc_start: 0.8440 (ttm) cc_final: 0.8231 (ttm)
REVERT: A  179 MET cc_start: 0.8538 (mmm) cc_final: 0.8014 (mmt)
REVERT: A  240 TRP cc_start: 0.5607 (m-10) cc_final: 0.4781 (p90)
REVERT: A  266 LEU cc_start: 0.8524 (tp) cc_final: 0.8321 (tp)
REVERT: A  405 MET cc_start: 0.6748 (mtp) cc_final: 0.6373 (mtp)
REVERT: B  145 VAL cc_start: 0.8790 (p) cc_final: 0.8579 (m)
REVERT: B  161 MET cc_start: 0.7753 (ttp) cc_final: 0.7014 (ttp)
REVERT: B  173 ASN cc_start: 0.8364 (m-40) cc_final: 0.7971 (t0)
REVERT: B  363 ILE cc_start: 0.8738 (mm) cc_final: 0.8218 (mt)
REVERT: C   10 LEU cc_start: 0.7938 (mt) cc_final: 0.7699 (mp)
REVERT: C  166 ASP cc_start: 0.8109 (t0) cc_final: 0.7807 (t0)
REVERT: D   66 ILE cc_start: 0.8906 (pt) cc_final: 0.8280 (mt)
REVERT: D   83 TYR cc_start: 0.7525 (t80) cc_final: 0.7234 (t80)
REVERT: E   27 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7448 (tm-30)
REVERT: E   28 TYR cc_start: 0.8689 (t80) cc_final: 0.8437 (t80)
REVERT: E   56 TYR cc_start: 0.7830 (t80) cc_final: 0.7147 (t80)
REVERT: E   63 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7638 (tptt)
REVERT: E   75 GLU cc_start: 0.8179 (pm20) cc_final: 0.7583 (mm-30)
REVERT: E   76 ARG cc_start: 0.6513 (mmm-85) cc_final: 0.6063 (mmt90)
  outliers start: 3
  outliers final: 2
  residues processed: 207
  average time/residue: 0.1008
  time to fit residues: 29.0559
Evaluate side-chains
  152 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 150
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain B residue  300 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0010
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A 269 ASN
A 321 ASN
A 331 GLN
A 342 GLN
A 361 ASN
A 373 ASN
A 467 GLN
A 602 GLN
B 133 GLN
C  36 GLN
C  57 GLN
C 108 GLN
C 124 ASN
C 162 GLN
D  59 ASN
D  62 ASN
D 200 ASN
D 218 ASN
D 241 ASN
D 245 GLN
D 281 ASN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.154626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123908 restraints weight = 17654.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.127004 restraints weight = 11344.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.129041 restraints weight = 8623.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130316 restraints weight = 7248.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131233 restraints weight = 6496.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10419  Z= 0.145
  Angle     :  0.601   9.467  14064  Z= 0.309
  Chirality :  0.040   0.176   1581
  Planarity :  0.004   0.043   1809
  Dihedral  :  4.794  32.500   1400
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.40 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.22), residues: 1274
  helix: -0.38 (0.19), residues: 718
  sheet: -2.18 (0.59), residues: 66
  loop : -2.60 (0.24), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  25 
 TYR   0.012   0.001   TYR D  83 
 PHE   0.019   0.001   PHE C  31 
 TRP   0.008   0.001   TRP E  71 
 HIS   0.005   0.001   HIS D 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10415)
  covalent geometry    : angle       0.59193 (14058)
  hydrogen bonds       : bond        0.04791 (  521)
  hydrogen bonds       : angle       4.64023 ( 1542)
  metal coordination   : bond        0.01044 (    4)
  metal coordination   : angle       5.10298 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.8630 (mmm) cc_final: 0.7966 (mmt)
REVERT: A  240 TRP cc_start: 0.5472 (m-10) cc_final: 0.4644 (p90)
REVERT: A  252 MET cc_start: 0.7689 (mmp) cc_final: 0.7484 (mmp)
REVERT: A  405 MET cc_start: 0.7054 (mtp) cc_final: 0.6746 (mtp)
REVERT: B  173 ASN cc_start: 0.8339 (m-40) cc_final: 0.7995 (t0)
REVERT: B  189 GLU cc_start: 0.7464 (tt0) cc_final: 0.7208 (tt0)
REVERT: C   10 LEU cc_start: 0.7909 (mt) cc_final: 0.7578 (mp)
REVERT: C   62 LEU cc_start: 0.7134 (mt) cc_final: 0.6868 (mt)
REVERT: D   66 ILE cc_start: 0.8839 (pt) cc_final: 0.8243 (mt)
REVERT: D   83 TYR cc_start: 0.7540 (t80) cc_final: 0.6984 (t80)
REVERT: E   12 LEU cc_start: 0.8824 (tt) cc_final: 0.8607 (mm)
REVERT: E   14 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8198 (mtpp)
REVERT: E   27 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: E   51 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8067 (tm-30)
REVERT: E   56 TYR cc_start: 0.7625 (t80) cc_final: 0.7408 (t80)
REVERT: E   62 PHE cc_start: 0.7088 (m-80) cc_final: 0.6628 (m-80)
REVERT: E   63 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7672 (tptt)
REVERT: E   75 GLU cc_start: 0.8125 (pm20) cc_final: 0.7633 (mm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 170
  average time/residue: 0.0920
  time to fit residues: 22.3771
Evaluate side-chains
  150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain E residue   41 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 37 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 106 optimal weight:   10.0000
   chunk 57 optimal weight:    0.7980
   chunk 116 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 126 optimal weight:    7.9990
   chunk 49 optimal weight:    0.0470
   overall best weight:    0.5880

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
C  36 GLN
D 253 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.155765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125167 restraints weight = 17768.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.128294 restraints weight = 11375.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.130329 restraints weight = 8604.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131448 restraints weight = 7220.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.132401 restraints weight = 6497.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10419  Z= 0.121
  Angle     :  0.552  10.327  14064  Z= 0.282
  Chirality :  0.039   0.168   1581
  Planarity :  0.004   0.038   1809
  Dihedral  :  4.532  34.776   1400
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.75 %
    Favored  : 82.18 %
  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: -1.14 (0.23), residues: 1274
  helix:  0.37 (0.20), residues: 718
  sheet: -1.90 (0.69), residues: 55
  loop : -2.31 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  76 
 TYR   0.009   0.001   TYR D  83 
 PHE   0.012   0.001   PHE C 179 
 TRP   0.008   0.001   TRP B 308 
 HIS   0.004   0.001   HIS D 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10415)
  covalent geometry    : angle       0.54511 (14058)
  hydrogen bonds       : bond        0.04322 (  521)
  hydrogen bonds       : angle       4.31320 ( 1542)
  metal coordination   : bond        0.00564 (    4)
  metal coordination   : angle       4.09638 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5480 (m-10) cc_final: 0.4621 (p90)
REVERT: A  405 MET cc_start: 0.6894 (mtp) cc_final: 0.6536 (mtp)
REVERT: B  173 ASN cc_start: 0.8294 (m-40) cc_final: 0.7853 (t0)
REVERT: B  189 GLU cc_start: 0.7490 (tt0) cc_final: 0.7192 (tt0)
REVERT: C   62 LEU cc_start: 0.7084 (mt) cc_final: 0.6877 (mt)
REVERT: D   66 ILE cc_start: 0.8839 (pt) cc_final: 0.8213 (mt)
REVERT: D  116 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7528 (t0)
REVERT: E   12 LEU cc_start: 0.8861 (tt) cc_final: 0.8618 (mm)
REVERT: E   14 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8220 (mtpp)
REVERT: E   27 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: E   55 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: E   62 PHE cc_start: 0.7259 (m-80) cc_final: 0.6723 (m-80)
REVERT: E   63 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7639 (tptt)
REVERT: E   75 GLU cc_start: 0.8106 (pm20) cc_final: 0.7667 (mm-30)
  outliers start: 23
  outliers final: 16
  residues processed: 170
  average time/residue: 0.0926
  time to fit residues: 22.2982
Evaluate side-chains
  159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain C residue   84 CYS
Chi-restraints excluded: chain D residue  116 ASP
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 124 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
A 336 HIS
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
C  36 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.154910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.124140 restraints weight = 17756.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.127185 restraints weight = 11407.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.129188 restraints weight = 8687.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130266 restraints weight = 7321.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.131134 restraints weight = 6603.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10419  Z= 0.136
  Angle     :  0.566   9.220  14064  Z= 0.287
  Chirality :  0.040   0.175   1581
  Planarity :  0.003   0.036   1809
  Dihedral  :  4.425  33.822   1398
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.29 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.23), residues: 1274
  helix:  0.65 (0.20), residues: 719
  sheet: -2.23 (0.61), residues: 66
  loop : -2.25 (0.25), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  25 
 TYR   0.019   0.001   TYR E  56 
 PHE   0.014   0.001   PHE C 179 
 TRP   0.009   0.001   TRP B 308 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10415)
  covalent geometry    : angle       0.56041 (14058)
  hydrogen bonds       : bond        0.04271 (  521)
  hydrogen bonds       : angle       4.25095 ( 1542)
  metal coordination   : bond        0.00646 (    4)
  metal coordination   : angle       3.85901 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5452 (m-10) cc_final: 0.4545 (p90)
REVERT: A  405 MET cc_start: 0.6808 (mtp) cc_final: 0.6505 (mtp)
REVERT: B  173 ASN cc_start: 0.8285 (m-40) cc_final: 0.7859 (t0)
REVERT: B  265 MET cc_start: 0.8425 (tpp) cc_final: 0.8047 (tpt)
REVERT: D   66 ILE cc_start: 0.8874 (pt) cc_final: 0.8277 (mt)
REVERT: E   12 LEU cc_start: 0.8914 (tt) cc_final: 0.8669 (mm)
REVERT: E   14 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8232 (mtpp)
REVERT: E   16 MET cc_start: 0.8168 (tpp) cc_final: 0.7768 (tpt)
REVERT: E   27 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: E   51 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7956 (tm-30)
REVERT: E   55 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: E   62 PHE cc_start: 0.7291 (m-80) cc_final: 0.6725 (m-80)
REVERT: E   75 GLU cc_start: 0.8043 (pm20) cc_final: 0.7612 (mm-30)
  outliers start: 31
  outliers final: 23
  residues processed: 168
  average time/residue: 0.0922
  time to fit residues: 21.9546
Evaluate side-chains
  159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  182 ILE
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 89 optimal weight:    0.1980
   chunk 93 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0050
   chunk 52 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 19 optimal weight:    0.0000
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.3600

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 HIS
C  36 GLN
D 125 GLN
D 246 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.157200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.126990 restraints weight = 17592.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130066 restraints weight = 11229.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.132096 restraints weight = 8510.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.133210 restraints weight = 7149.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.134073 restraints weight = 6429.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10419  Z= 0.106
  Angle     :  0.539   9.474  14064  Z= 0.272
  Chirality :  0.039   0.163   1581
  Planarity :  0.003   0.040   1809
  Dihedral  :  4.264  35.182   1398
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.91 %
    Favored  : 79.30 %
  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: -0.57 (0.24), residues: 1274
  helix:  0.93 (0.20), residues: 721
  sheet: -2.19 (0.60), residues: 66
  loop : -2.15 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  32 
 TYR   0.026   0.001   TYR E  56 
 PHE   0.008   0.001   PHE A 347 
 TRP   0.007   0.001   TRP B 308 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (10415)
  covalent geometry    : angle       0.53430 (14058)
  hydrogen bonds       : bond        0.03910 (  521)
  hydrogen bonds       : angle       4.04720 ( 1542)
  metal coordination   : bond        0.00310 (    4)
  metal coordination   : angle       3.30856 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5531 (m-10) cc_final: 0.4552 (p90)
REVERT: B  173 ASN cc_start: 0.8267 (m-40) cc_final: 0.7890 (t0)
REVERT: B  189 GLU cc_start: 0.7620 (tt0) cc_final: 0.7233 (tt0)
REVERT: B  265 MET cc_start: 0.8525 (tpp) cc_final: 0.8159 (tpt)
REVERT: D   66 ILE cc_start: 0.8857 (pt) cc_final: 0.8213 (mt)
REVERT: E   27 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7454 (tm-30)
REVERT: E   51 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: E   55 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: E   62 PHE cc_start: 0.7389 (m-80) cc_final: 0.6931 (m-80)
REVERT: E   75 GLU cc_start: 0.8025 (pm20) cc_final: 0.7655 (mm-30)
  outliers start: 31
  outliers final: 18
  residues processed: 174
  average time/residue: 0.0838
  time to fit residues: 21.5792
Evaluate side-chains
  163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 118 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0020
   chunk 75 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 GLN
A 559 HIS
B 133 GLN
B 326 GLN
E  35 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.153076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125230 restraints weight = 17923.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126385 restraints weight = 12048.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.126434 restraints weight = 9537.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126703 restraints weight = 9793.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126862 restraints weight = 9264.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10419  Z= 0.173
  Angle     :  0.611   9.622  14064  Z= 0.304
  Chirality :  0.041   0.174   1581
  Planarity :  0.004   0.036   1809
  Dihedral  :  4.340  30.980   1398
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 18.18 %
    Favored  : 78.85 %
  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: -0.58 (0.23), residues: 1274
  helix:  0.90 (0.20), residues: 719
  sheet: -2.13 (0.60), residues: 66
  loop : -2.13 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 568 
 TYR   0.027   0.002   TYR E  28 
 PHE   0.011   0.001   PHE B 168 
 TRP   0.012   0.001   TRP B 308 
 HIS   0.008   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10415)
  covalent geometry    : angle       0.60532 (14058)
  hydrogen bonds       : bond        0.04392 (  521)
  hydrogen bonds       : angle       4.19902 ( 1542)
  metal coordination   : bond        0.00930 (    4)
  metal coordination   : angle       3.99828 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 142
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  240 TRP cc_start: 0.5543 (m-10) cc_final: 0.4458 (p90)
REVERT: B  173 ASN cc_start: 0.8299 (m-40) cc_final: 0.7837 (t0)
REVERT: B  265 MET cc_start: 0.8480 (tpp) cc_final: 0.8110 (tpt)
REVERT: B  308 TRP cc_start: 0.8339 (p-90) cc_final: 0.8120 (p-90)
REVERT: D   66 ILE cc_start: 0.8882 (pt) cc_final: 0.8308 (mt)
REVERT: D  261 ILE cc_start: 0.7920 (tt) cc_final: 0.7713 (tt)
REVERT: E   14 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8294 (mtpp)
REVERT: E   27 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: E   51 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: E   55 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: E   62 PHE cc_start: 0.7659 (m-80) cc_final: 0.7084 (m-80)
REVERT: E   75 GLU cc_start: 0.8125 (pm20) cc_final: 0.7604 (mm-30)
  outliers start: 33
  outliers final: 26
  residues processed: 163
  average time/residue: 0.0801
  time to fit residues: 19.2352
Evaluate side-chains
  162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  326 GLN
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 95 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0270
   chunk 116 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 3 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
D  73 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.155084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124517 restraints weight = 17672.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.127544 restraints weight = 11383.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129469 restraints weight = 8662.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.130590 restraints weight = 7329.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.131508 restraints weight = 6612.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10419  Z= 0.124
  Angle     :  0.579   8.738  14064  Z= 0.287
  Chirality :  0.040   0.181   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.268  32.601   1398
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.18 %
    Favored  : 78.67 %
  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: -0.44 (0.24), residues: 1274
  helix:  1.02 (0.20), residues: 722
  sheet: -2.18 (0.58), residues: 66
  loop : -2.09 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 325 
 TYR   0.021   0.001   TYR E  56 
 PHE   0.011   0.001   PHE A 367 
 TRP   0.010   0.001   TRP B 308 
 HIS   0.006   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10415)
  covalent geometry    : angle       0.57491 (14058)
  hydrogen bonds       : bond        0.04122 (  521)
  hydrogen bonds       : angle       4.06865 ( 1542)
  metal coordination   : bond        0.00450 (    4)
  metal coordination   : angle       3.45214 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 145
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8659 (ptm160)
REVERT: A  240 TRP cc_start: 0.5427 (m-10) cc_final: 0.4431 (p90)
REVERT: B  173 ASN cc_start: 0.8236 (m-40) cc_final: 0.7800 (t0)
REVERT: B  265 MET cc_start: 0.8403 (tpp) cc_final: 0.8067 (tpt)
REVERT: D   66 ILE cc_start: 0.8886 (pt) cc_final: 0.8269 (mt)
REVERT: E   27 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7517 (tm-30)
REVERT: E   51 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: E   55 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7849 (mt-10)
REVERT: E   62 PHE cc_start: 0.7365 (m-80) cc_final: 0.6905 (m-80)
REVERT: E   75 GLU cc_start: 0.8058 (pm20) cc_final: 0.7718 (mm-30)
  outliers start: 35
  outliers final: 27
  residues processed: 170
  average time/residue: 0.0846
  time to fit residues: 21.1232
Evaluate side-chains
  167 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  492 CYS
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   74 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 110 optimal weight:    5.9990
   chunk 108 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 GLN
A 559 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.152930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122075 restraints weight = 17806.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.124915 restraints weight = 11790.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.126548 restraints weight = 9109.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.127767 restraints weight = 7829.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.128655 restraints weight = 7060.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10419  Z= 0.164
  Angle     :  0.609   7.946  14064  Z= 0.302
  Chirality :  0.041   0.166   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.329  30.469   1398
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.99 %
    Favored  : 77.95 %
  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: -0.48 (0.24), residues: 1274
  helix:  0.99 (0.20), residues: 722
  sheet: -2.29 (0.57), residues: 66
  loop : -2.08 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 359 
 TYR   0.018   0.001   TYR D  83 
 PHE   0.012   0.001   PHE C 160 
 TRP   0.012   0.001   TRP B 159 
 HIS   0.004   0.001   HIS D 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10415)
  covalent geometry    : angle       0.60411 (14058)
  hydrogen bonds       : bond        0.04356 (  521)
  hydrogen bonds       : angle       4.23763 ( 1542)
  metal coordination   : bond        0.00829 (    4)
  metal coordination   : angle       3.77135 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8719 (ptm160)
REVERT: A  240 TRP cc_start: 0.5419 (m-10) cc_final: 0.4361 (p90)
REVERT: B  173 ASN cc_start: 0.8277 (m-40) cc_final: 0.7883 (t0)
REVERT: B  265 MET cc_start: 0.8491 (tpp) cc_final: 0.8132 (tpt)
REVERT: D   66 ILE cc_start: 0.8900 (pt) cc_final: 0.8303 (mt)
REVERT: E   27 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: E   51 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: E   55 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: E   62 PHE cc_start: 0.7457 (m-80) cc_final: 0.6971 (m-80)
REVERT: E   75 GLU cc_start: 0.8107 (pm20) cc_final: 0.7727 (mm-30)
  outliers start: 34
  outliers final: 27
  residues processed: 164
  average time/residue: 0.0798
  time to fit residues: 19.5701
Evaluate side-chains
  161 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Chi-restraints excluded: chain E residue   42 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 4 optimal weight:    0.3980
   chunk 81 optimal weight:    0.9980
   chunk 116 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 HIS
C  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.154278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.123508 restraints weight = 17781.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.126407 restraints weight = 11603.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.128321 restraints weight = 8945.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129376 restraints weight = 7578.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.130175 restraints weight = 6854.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10419  Z= 0.134
  Angle     :  0.593   7.888  14064  Z= 0.294
  Chirality :  0.040   0.187   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.314  31.727   1398
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.89 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.24), residues: 1274
  helix:  1.07 (0.20), residues: 723
  sheet: -2.22 (0.58), residues: 66
  loop : -2.01 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 359 
 TYR   0.025   0.001   TYR E  56 
 PHE   0.018   0.001   PHE A 275 
 TRP   0.008   0.001   TRP B 308 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10415)
  covalent geometry    : angle       0.58957 (14058)
  hydrogen bonds       : bond        0.04207 (  521)
  hydrogen bonds       : angle       4.13670 ( 1542)
  metal coordination   : bond        0.00526 (    4)
  metal coordination   : angle       3.34839 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8686 (ptm160)
REVERT: A  240 TRP cc_start: 0.5526 (m-10) cc_final: 0.4425 (p90)
REVERT: B  173 ASN cc_start: 0.8277 (m-40) cc_final: 0.7874 (t0)
REVERT: B  265 MET cc_start: 0.8463 (tpp) cc_final: 0.8118 (tpt)
REVERT: D   66 ILE cc_start: 0.8874 (pt) cc_final: 0.8278 (mt)
REVERT: E   27 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7391 (tm-30)
REVERT: E   51 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: E   55 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7910 (mt-10)
REVERT: E   62 PHE cc_start: 0.7461 (m-80) cc_final: 0.6951 (m-80)
REVERT: E   75 GLU cc_start: 0.8112 (pm20) cc_final: 0.7735 (mm-30)
  outliers start: 28
  outliers final: 25
  residues processed: 153
  average time/residue: 0.0749
  time to fit residues: 17.4558
Evaluate side-chains
  160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 118 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 124 optimal weight:    8.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 559 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 = 0.4087 r_free = 0.4087 target = 0.154365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.123619 restraints weight = 17544.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.126521 restraints weight = 11512.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.128386 restraints weight = 8894.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129432 restraints weight = 7559.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.129706 restraints weight = 6863.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10419  Z= 0.137
  Angle     :  0.597   8.089  14064  Z= 0.298
  Chirality :  0.040   0.195   1581
  Planarity :  0.003   0.035   1809
  Dihedral  :  4.301  31.440   1398
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.53 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.30 (0.24), residues: 1274
  helix:  1.10 (0.20), residues: 722
  sheet: -2.16 (0.59), residues: 66
  loop : -1.94 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 359 
 TYR   0.031   0.001   TYR E  28 
 PHE   0.012   0.001   PHE A 275 
 TRP   0.008   0.001   TRP B 159 
 HIS   0.007   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10415)
  covalent geometry    : angle       0.59293 (14058)
  hydrogen bonds       : bond        0.04205 (  521)
  hydrogen bonds       : angle       4.13947 ( 1542)
  metal coordination   : bond        0.00538 (    4)
  metal coordination   : angle       3.37983 (    6)

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

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

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2548 Ramachandran restraints generated.
    1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A  181 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8599 (ptm160)
REVERT: A  240 TRP cc_start: 0.5556 (m-10) cc_final: 0.4446 (p90)
REVERT: B  173 ASN cc_start: 0.8255 (m-40) cc_final: 0.7862 (t0)
REVERT: B  265 MET cc_start: 0.8465 (tpp) cc_final: 0.8121 (tpt)
REVERT: D   66 ILE cc_start: 0.8862 (pt) cc_final: 0.8247 (mt)
REVERT: E   27 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7387 (tm-30)
REVERT: E   51 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: E   55 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7890 (mt-10)
REVERT: E   62 PHE cc_start: 0.7423 (m-80) cc_final: 0.6963 (m-80)
REVERT: E   75 GLU cc_start: 0.8119 (pm20) cc_final: 0.7750 (mm-30)
  outliers start: 27
  outliers final: 26
  residues processed: 155
  average time/residue: 0.0778
  time to fit residues: 18.1431
Evaluate side-chains
  159 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  181 ARG
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain A residue  559 HIS
Chi-restraints excluded: chain A residue  579 VAL
Chi-restraints excluded: chain A residue  627 GLU
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue  178 PHE
Chi-restraints excluded: chain D residue  205 VAL
Chi-restraints excluded: chain D residue  217 THR
Chi-restraints excluded: chain D residue  225 ILE
Chi-restraints excluded: chain D residue  226 LEU
Chi-restraints excluded: chain E residue   37 LEU
Chi-restraints excluded: chain E residue   41 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 109 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 126 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 107 optimal weight:   10.0000
   chunk 112 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 HIS
C  36 GLN
C 124 ASN
C 144 GLN
D 127 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.150102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.118849 restraints weight = 17941.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.121637 restraints weight = 11958.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.123418 restraints weight = 9286.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124609 restraints weight = 7946.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125208 restraints weight = 7169.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10419  Z= 0.228
  Angle     :  0.674   8.521  14064  Z= 0.337
  Chirality :  0.043   0.194   1581
  Planarity :  0.004   0.041   1809
  Dihedral  :  4.554  27.971   1398
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.07 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.24), residues: 1274
  helix:  0.87 (0.20), residues: 718
  sheet: -2.23 (0.59), residues: 66
  loop : -1.98 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 359 
 TYR   0.023   0.002   TYR D  83 
 PHE   0.014   0.002   PHE C 160 
 TRP   0.015   0.002   TRP B 159 
 HIS   0.005   0.002   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00548 (10415)
  covalent geometry    : angle       0.66864 (14058)
  hydrogen bonds       : bond        0.04865 (  521)
  hydrogen bonds       : angle       4.46697 ( 1542)
  metal coordination   : bond        0.01327 (    4)
  metal coordination   : angle       3.98344 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1579.44 seconds
wall clock time: 28 minutes 4.68 seconds (1684.68 seconds total)