Starting phenix.real_space_refine
on Sat Aug 23 09:53:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jbe_36143/08_2025/8jbe_36143.cif"
  }
  resolution = 3.25
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    7240      2.51       5
     N    1923      2.21       5
     O    2042      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11260
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4674
          Classifications: {'peptide': 591}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 566}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 391, 3206
          Classifications: {'peptide': 391}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 375}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 3380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 418, 3380
          Classifications: {'peptide': 418}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 404}
  Time building chain proxies: 2.47, per 1000 atoms: 0.22
  Number of scatterers: 11260
  At special positions: 0
  Unit cell: (68.85, 120.7, 188.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    2042      8.00
     N    1923      7.00
     C    7240      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: 0.86
  Conformation dependent library (CDL) restraints added in 382.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2684

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 13 sheets defined
      39.7% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.573A  pdb=" N   ALA A  45 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.572A  pdb=" N   ILE A 108 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 355 through 363
      removed outlier: 3.727A  pdb=" N   LEU A 359 " --> pdb=" O   CYS A 355 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 374
    Processing helix  chain 'A' and resid 380 through 392
      removed outlier: 3.509A  pdb=" N   LYS A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 427
      removed outlier: 3.611A  pdb=" N   LYS A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   TYR A 414 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ALA A 415 " --> pdb=" O   ASN A 411 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A 420 " --> pdb=" O   SER A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 458
      removed outlier: 3.652A  pdb=" N   MET A 452 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN A 454 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ILE A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ARG A 458 " --> pdb=" O   GLN A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 479
      removed outlier: 3.710A  pdb=" N   ILE A 468 " --> pdb=" O   TYR A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 498
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 516 through 527
      removed outlier: 3.978A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 522 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   SER A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 544
      removed outlier: 3.666A  pdb=" N   ILE A 544 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 558
      removed outlier: 3.682A  pdb=" N   ILE A 550 " --> pdb=" O   ALA A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 571
      removed outlier: 3.561A  pdb=" N   ASN A 569 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 3.665A  pdb=" N   THR A 588 " --> pdb=" O   ALA A 584 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LYS A 589 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 610
    Processing helix  chain 'A' and resid 620 through 631
    Processing helix  chain 'B' and resid 28 through 31
    Processing helix  chain 'B' and resid 42 through 61
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.841A  pdb=" N   CYS B  69 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 137
      removed outlier: 4.028A  pdb=" N   TYR B 121 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 157
      removed outlier: 3.546A  pdb=" N   LEU B 155 " --> pdb=" O   LYS B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 160
      No H-bonds generated for 'chain 'B' and resid 158 through 160'
    Processing helix  chain 'B' and resid 178 through 184
    Processing helix  chain 'B' and resid 192 through 201
    Processing helix  chain 'B' and resid 204 through 209
    Processing helix  chain 'B' and resid 230 through 245
    Processing helix  chain 'B' and resid 332 through 361
      removed outlier: 3.747A  pdb=" N   TYR B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
      Proline residue:  B 345  - end of helix
    Processing helix  chain 'B' and resid 407 through 417
      removed outlier: 3.553A  pdb=" N   ALA B 415 " --> pdb=" O   ILE B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 477
    Processing helix  chain 'C' and resid 139 through 155
    Processing helix  chain 'C' and resid 189 through 208
      removed outlier: 3.607A  pdb=" N   LEU C 193 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 219
    Processing helix  chain 'C' and resid 232 through 242
      removed outlier: 3.971A  pdb=" N   PHE C 236 " --> pdb=" O   SER C 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 259
      removed outlier: 3.549A  pdb=" N   THR C 258 " --> pdb=" O   PHE C 254 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 282
    Processing helix  chain 'C' and resid 311 through 325
    Processing helix  chain 'C' and resid 373 through 390
      removed outlier: 3.723A  pdb=" N   SER C 390 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 402
      removed outlier: 3.792A  pdb=" N   ALA C 395 " --> pdb=" O   HIS C 391 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN C 402 " --> pdb=" O   GLU C 398 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 414
    Processing helix  chain 'C' and resid 443 through 461
    Processing helix  chain 'C' and resid 498 through 516
      removed outlier: 3.875A  pdb=" N   VAL C 502 " --> pdb=" O   ASP C 498 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 516 through 521
      removed outlier: 4.018A  pdb=" N   TYR C 520 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18
      removed outlier: 3.530A  pdb=" N   ILE A  17 " --> pdb=" O   MET A 349 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   MET A 349 " --> pdb=" O   ILE A  17 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL A 341 " --> pdb=" O   TRP A 350 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL A 334 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 31
    Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 124
      removed outlier: 6.410A  pdb=" N   GLU A 127 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 142
      removed outlier: 7.361A  pdb=" N   VAL A 138 " --> pdb=" O   VAL A 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 162
      removed outlier: 4.122A  pdb=" N   TRP A 160 " --> pdb=" O   CYS A 173 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 191 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215
      removed outlier: 8.259A  pdb=" N   MET A 233 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   ARG A 254 " --> pdb=" O   MET A 233 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 252 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   VAL A 252 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   VAL A 237 " --> pdb=" O   CYS A 250 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   CYS A 250 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   THR A 296 " --> pdb=" O   CYS A 250 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 266
    Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 37
      removed outlier: 6.319A  pdb=" N   ILE B  17 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   TYR B  36 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   PHE B  15 " --> pdb=" O   TYR B  36 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B  12 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ASN B  95 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER B  14 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B  80 " --> pdb=" O   LEU B  92 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR B  78 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   THR B  77 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS C 164 " --> pdb=" O   ALA B  71 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   THR C 161 " --> pdb=" O   PHE C 172 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE C 179 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE C 130 " --> pdb=" O   ILE C 121 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 186 through 187
      removed outlier: 6.127A  pdb=" N   ILE B 186 " --> pdb=" O   HIS B 391 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   THR B 393 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLN B 390 " --> pdb=" O   ASN B 385 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN B 385 " --> pdb=" O   GLN B 390 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ARG B 445 " --> pdb=" O   GLU B 429 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU B 429 " --> pdb=" O   ARG B 445 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   GLU B 430 " --> pdb=" O   GLU C 472 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLU C 472 " --> pdb=" O   GLU B 430 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   GLN B 432 " --> pdb=" O   ILE C 470 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ILE C 470 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   LYS B 434 " --> pdb=" O   LYS C 468 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LYS C 468 " --> pdb=" O   ALA C 483 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE C 470 " --> pdb=" O   ALA C 481 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   GLU C 488 " --> pdb=" O   TYR C 423 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   TYR C 423 " --> pdb=" O   GLU C 488 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   TYR C 490 " --> pdb=" O   PHE C 421 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE C 421 " --> pdb=" O   TYR C 490 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ILE C 492 " --> pdb=" O   ARG C 419 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 223 through 225
      removed outlier: 8.214A  pdb=" N   ILE B 212 " --> pdb=" O   ASN B 325 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   ASN B 325 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU B 214 " --> pdb=" O   PHE B 323 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 261 through 262
      removed outlier: 6.512A  pdb=" N   ILE C 261 " --> pdb=" O   LEU C 431 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 333 through 337
      removed outlier: 3.784A  pdb=" N   PHE C 290 " --> pdb=" O   LEU C 366 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   VAL C 289 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   ARG C 304 " --> pdb=" O   VAL C 289 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA C 291 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU C 302 " --> pdb=" O   ALA C 291 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   LEU C 293 " --> pdb=" O   ILE C 300 " (cutoff:3.500A)
      removed outlier: 9.232A  pdb=" N   ALA C 526 " --> pdb=" O   ILE C 300 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU C 302 " --> pdb=" O   ALA C 526 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1455 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: 1.67

  Time building geometry restraints manager: 1.08 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: 3626
        1.34 -     1.46: 1588
        1.46 -     1.57: 6190
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 11484
  Sorted by residual:
  bond pdb=" CA  GLU A 137 "
       pdb=" C   GLU A 137 "
    ideal  model  delta    sigma   weight residual
    1.530  1.502  0.028 9.10e-03 1.21e+04 9.39e+00
  bond pdb=" CA  GLU A 137 "
       pdb=" CB  GLU A 137 "
    ideal  model  delta    sigma   weight residual
    1.542  1.521  0.022 8.90e-03 1.26e+04 5.89e+00
  bond pdb=" CA  ASN A 133 "
       pdb=" C   ASN A 133 "
    ideal  model  delta    sigma   weight residual
    1.524  1.502  0.022 1.24e-02 6.50e+03 3.14e+00
  bond pdb=" C   ASN A 133 "
       pdb=" O   ASN A 133 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.017 1.15e-02 7.56e+03 2.11e+00
  bond pdb=" CA  THR A 134 "
       pdb=" C   THR A 134 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.018 1.34e-02 5.57e+03 1.76e+00
  ... (remaining 11479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 15257
        1.82 -     3.63: 243
        3.63 -     5.45: 26
        5.45 -     7.26: 6
        7.26 -     9.08: 2
  Bond angle restraints: 15534
  Sorted by residual:
  angle pdb=" C   VAL A 138 "
        pdb=" N   TYR A 139 "
        pdb=" CA  TYR A 139 "
      ideal   model   delta    sigma   weight residual
     123.03  115.04    7.99 1.79e+00 3.12e-01 1.99e+01
  angle pdb=" C   GLU A 137 "
        pdb=" CA  GLU A 137 "
        pdb=" CB  GLU A 137 "
      ideal   model   delta    sigma   weight residual
     114.87  109.18    5.69 1.51e+00 4.39e-01 1.42e+01
  angle pdb=" CA  GLU B   9 "
        pdb=" CB  GLU B   9 "
        pdb=" CG  GLU B   9 "
      ideal   model   delta    sigma   weight residual
     114.10  121.04   -6.94 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" N   LYS A 152 "
        pdb=" CA  LYS A 152 "
        pdb=" C   LYS A 152 "
      ideal   model   delta    sigma   weight residual
     108.19  111.89   -3.70 1.29e+00 6.01e-01 8.23e+00
  angle pdb=" N   GLN B 158 "
        pdb=" CA  GLN B 158 "
        pdb=" C   GLN B 158 "
      ideal   model   delta    sigma   weight residual
     113.21  110.06    3.15 1.15e+00 7.56e-01 7.49e+00
  ... (remaining 15529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 6267
       17.54 -    35.09: 539
       35.09 -    52.63: 117
       52.63 -    70.18: 14
       70.18 -    87.72: 13
  Dihedral angle restraints: 6950
    sinusoidal: 2829
      harmonic: 4121
  Sorted by residual:
  dihedral pdb=" CA  GLN B 158 "
           pdb=" C   GLN B 158 "
           pdb=" N   LYS B 159 "
           pdb=" CA  LYS B 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  HIS A 526 "
           pdb=" C   HIS A 526 "
           pdb=" N   SER A 527 "
           pdb=" CA  SER A 527 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.65   18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  MET A  65 "
           pdb=" C   MET A  65 "
           pdb=" N   SER A  66 "
           pdb=" CA  SER A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.12  -16.88     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 6947 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1198
       0.037 -    0.074: 420
       0.074 -    0.111: 131
       0.111 -    0.149: 34
       0.149 -    0.186: 3
  Chirality restraints: 1786
  Sorted by residual:
  chirality pdb=" CA  GLU B   9 "
            pdb=" N   GLU B   9 "
            pdb=" C   GLU B   9 "
            pdb=" CB  GLU B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" CG  LEU B  72 "
            pdb=" CB  LEU B  72 "
            pdb=" CD1 LEU B  72 "
            pdb=" CD2 LEU B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  ILE B  17 "
            pdb=" N   ILE B  17 "
            pdb=" C   ILE B  17 "
            pdb=" CB  ILE B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.57e-01
  ... (remaining 1783 not shown)

  Planarity restraints: 1965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 127 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO C 128 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO C 128 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 128 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 181 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.70e+00
        pdb=" N   PRO A 182 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 182 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 182 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 414 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   TYR A 414 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   TYR A 414 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 415 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1962 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1153
        2.75 -     3.29: 10560
        3.29 -     3.82: 17238
        3.82 -     4.36: 19532
        4.36 -     4.90: 35942
  Nonbonded interactions: 84425
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 524 "
            pdb=" OG  SER A 527 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   PHE C 264 "
            pdb=" NH2 ARG C 271 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OE2 GLU C 488 "
            pdb=" OH  TYR C 490 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OH  TYR B  36 "
            pdb=" OD2 ASP B  49 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OH  TYR A   9 "
            pdb=" O   SER A 280 "
     model   vdw
     2.252 3.040
  ... (remaining 84420 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.200
  Find NCS groups from input model:        0.060
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
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      :  0.003   0.031  11484  Z= 0.159
  Angle     :  0.577   9.079  15534  Z= 0.316
  Chirality :  0.043   0.186   1786
  Planarity :  0.004   0.041   1965
  Dihedral  : 14.009  87.723   4266
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.69 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  0.40 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole: -0.14 (0.24), residues: 1372
  helix:  1.47 (0.24), residues: 525
  sheet: -0.39 (0.32), residues: 303
  loop : -1.48 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 499 
 TYR   0.017   0.001   TYR C 453 
 PHE   0.019   0.001   PHE A  63 
 TRP   0.023   0.002   TRP A 350 
 HIS   0.005   0.001   HIS B 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11484)
  covalent geometry    : angle       0.57704 (15534)
  hydrogen bonds       : bond        0.19022 (  510)
  hydrogen bonds       : angle       6.43450 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  172 LEU cc_start: 0.8442 (mp) cc_final: 0.8222 (mp)
REVERT: A  240 LEU cc_start: 0.8181 (mt) cc_final: 0.7963 (tt)
REVERT: B  277 ARG cc_start: 0.6210 (mmt-90) cc_final: 0.3430 (mmm160)
  outliers start: 5
  outliers final: 2
  residues processed: 128
  average time/residue: 0.0931
  time to fit residues: 17.3082
Evaluate side-chains
  99 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  154 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
C 115 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.144554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110839 restraints weight = 16931.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 3.35
r_work: 0.3278 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11484  Z= 0.165
  Angle     :  0.575   8.201  15534  Z= 0.304
  Chirality :  0.045   0.164   1786
  Planarity :  0.004   0.053   1965
  Dihedral  :  4.762  49.263   1512
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.32 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.27 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole: -0.00 (0.24), residues: 1372
  helix:  1.51 (0.24), residues: 529
  sheet: -0.24 (0.31), residues: 316
  loop : -1.40 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  73 
 TYR   0.014   0.002   TYR B  16 
 PHE   0.014   0.002   PHE C 264 
 TRP   0.026   0.002   TRP A 350 
 HIS   0.004   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (11484)
  covalent geometry    : angle       0.57504 (15534)
  hydrogen bonds       : bond        0.05129 (  510)
  hydrogen bonds       : angle       4.76378 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 TRP cc_start: 0.8526 (m-90) cc_final: 0.8220 (m-90)
REVERT: A  417 TRP cc_start: 0.6203 (p-90) cc_final: 0.5885 (p-90)
REVERT: B  277 ARG cc_start: 0.6418 (mmt-90) cc_final: 0.3437 (mmm160)
REVERT: C  311 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7423 (m90)
  outliers start: 9
  outliers final: 6
  residues processed: 102
  average time/residue: 0.1080
  time to fit residues: 15.7299
Evaluate side-chains
  98 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  452 MET
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  311 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
C 311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.142889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.108602 restraints weight = 17123.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.48
r_work: 0.3236 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  11484  Z= 0.196
  Angle     :  0.590   8.236  15534  Z= 0.311
  Chirality :  0.045   0.156   1786
  Planarity :  0.004   0.040   1965
  Dihedral  :  4.750  45.687   1512
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.05 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 10.17 %
    Favored  : 88.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole: -0.03 (0.24), residues: 1372
  helix:  1.44 (0.24), residues: 528
  sheet: -0.20 (0.32), residues: 313
  loop : -1.38 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 461 
 TYR   0.014   0.002   TYR C 423 
 PHE   0.016   0.002   PHE C 170 
 TRP   0.019   0.002   TRP A 350 
 HIS   0.007   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 (11484)
  covalent geometry    : angle       0.58997 (15534)
  hydrogen bonds       : bond        0.05435 (  510)
  hydrogen bonds       : angle       4.59542 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8256 (tpt90)
REVERT: A  350 TRP cc_start: 0.8483 (m-90) cc_final: 0.8060 (m-90)
  outliers start: 11
  outliers final: 7
  residues processed: 103
  average time/residue: 0.1090
  time to fit residues: 15.8463
Evaluate side-chains
  97 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  311 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
A 411 ASN
C 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.142770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108417 restraints weight = 17093.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 3.81
r_work: 0.3246 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11484  Z= 0.186
  Angle     :  0.574   7.995  15534  Z= 0.303
  Chirality :  0.045   0.261   1786
  Planarity :  0.004   0.039   1965
  Dihedral  :  4.702  43.316   1512
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.98 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.91 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.02 (0.24), residues: 1372
  helix:  1.45 (0.24), residues: 528
  sheet: -0.12 (0.32), residues: 314
  loop : -1.36 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 461 
 TYR   0.017   0.002   TYR A 609 
 PHE   0.015   0.002   PHE C 264 
 TRP   0.017   0.002   TRP A 350 
 HIS   0.006   0.001   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (11484)
  covalent geometry    : angle       0.57441 (15534)
  hydrogen bonds       : bond        0.05161 (  510)
  hydrogen bonds       : angle       4.46537 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8246 (tpt90)
REVERT: A  350 TRP cc_start: 0.8547 (m-90) cc_final: 0.7992 (m-90)
REVERT: C  152 PHE cc_start: 0.7893 (t80) cc_final: 0.7488 (t80)
REVERT: C  401 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7152 (mp10)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1239
  time to fit residues: 17.9556
Evaluate side-chains
  97 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  311 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0050
   chunk 92 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 10 optimal weight:   20.0000
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
A 214 GLN
** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.144302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.110329 restraints weight = 16535.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 3.43
r_work: 0.3271 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11484  Z= 0.116
  Angle     :  0.511   8.005  15534  Z= 0.272
  Chirality :  0.043   0.246   1786
  Planarity :  0.003   0.039   1965
  Dihedral  :  4.486  41.340   1512
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.39 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.19 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.28 (0.24), residues: 1372
  helix:  1.70 (0.24), residues: 528
  sheet:  0.03 (0.32), residues: 313
  loop : -1.27 (0.28), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 152 
 TYR   0.018   0.001   TYR A 609 
 PHE   0.012   0.001   PHE C 264 
 TRP   0.015   0.002   TRP A 350 
 HIS   0.004   0.001   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11484)
  covalent geometry    : angle       0.51081 (15534)
  hydrogen bonds       : bond        0.04127 (  510)
  hydrogen bonds       : angle       4.25896 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.9002 (mm) cc_final: 0.8727 (tp)
REVERT: A  350 TRP cc_start: 0.8505 (m-90) cc_final: 0.7950 (m-90)
REVERT: C  152 PHE cc_start: 0.7842 (t80) cc_final: 0.7594 (t80)
REVERT: C  401 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7169 (mp10)
  outliers start: 14
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1103
  time to fit residues: 15.4386
Evaluate side-chains
  93 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue  481 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 8 optimal weight:   30.0000
   chunk 110 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 118 HIS
A 214 GLN
B  39 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.140270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.098211 restraints weight = 16744.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.47
r_work: 0.3246 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  11484  Z= 0.250
  Angle     :  0.624   8.509  15534  Z= 0.326
  Chirality :  0.047   0.327   1786
  Planarity :  0.004   0.040   1965
  Dihedral  :  4.618  41.438   1510
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.71 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.66 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole: -0.00 (0.24), residues: 1372
  helix:  1.36 (0.24), residues: 528
  sheet: -0.06 (0.32), residues: 314
  loop : -1.35 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 461 
 TYR   0.018   0.002   TYR A 609 
 PHE   0.018   0.002   PHE A 601 
 TRP   0.016   0.002   TRP A 350 
 HIS   0.005   0.001   HIS C 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 (11484)
  covalent geometry    : angle       0.62356 (15534)
  hydrogen bonds       : bond        0.05850 (  510)
  hydrogen bonds       : angle       4.50196 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.8944 (mm) cc_final: 0.8643 (tp)
REVERT: A   77 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6523 (t80)
REVERT: A  350 TRP cc_start: 0.8551 (m-90) cc_final: 0.7922 (m-90)
REVERT: C  401 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7372 (mp10)
  outliers start: 27
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0940
  time to fit residues: 15.7958
Evaluate side-chains
  109 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  343 MET
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  311 HIS
Chi-restraints excluded: chain C residue  479 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 124 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 104 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.143788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.109896 restraints weight = 17093.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 3.48
r_work: 0.3252 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11484  Z= 0.131
  Angle     :  0.535   8.258  15534  Z= 0.283
  Chirality :  0.043   0.225   1786
  Planarity :  0.003   0.038   1965
  Dihedral  :  4.426  42.463   1510
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.25 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.82 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.20 (0.24), residues: 1372
  helix:  1.62 (0.24), residues: 528
  sheet: -0.05 (0.31), residues: 319
  loop : -1.28 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 152 
 TYR   0.023   0.001   TYR A 609 
 PHE   0.012   0.001   PHE C 264 
 TRP   0.031   0.002   TRP A 417 
 HIS   0.003   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11484)
  covalent geometry    : angle       0.53502 (15534)
  hydrogen bonds       : bond        0.04412 (  510)
  hydrogen bonds       : angle       4.25110 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.8956 (mm) cc_final: 0.8686 (tp)
REVERT: A   77 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6490 (t80)
REVERT: A   95 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.5366 (t80)
REVERT: A  350 TRP cc_start: 0.8614 (m-90) cc_final: 0.8032 (m-90)
REVERT: B  229 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8588 (mp)
REVERT: C  401 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7336 (mp10)
  outliers start: 27
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0954
  time to fit residues: 15.8032
Evaluate side-chains
  103 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  343 MET
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  311 HIS
Chi-restraints excluded: chain C residue  479 VAL
Chi-restraints excluded: chain C residue  502 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 72 optimal weight:    0.4980
   chunk 106 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 626 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.141821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.108043 restraints weight = 16919.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 3.44
r_work: 0.3221 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11484  Z= 0.201
  Angle     :  0.612  10.946  15534  Z= 0.318
  Chirality :  0.045   0.218   1786
  Planarity :  0.004   0.039   1965
  Dihedral  :  4.530  41.485   1510
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.63 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.30 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.04 (0.24), residues: 1372
  helix:  1.45 (0.24), residues: 528
  sheet: -0.11 (0.31), residues: 321
  loop : -1.34 (0.27), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 152 
 TYR   0.024   0.002   TYR A 609 
 PHE   0.032   0.002   PHE C 328 
 TRP   0.017   0.002   TRP A 417 
 HIS   0.004   0.001   HIS C 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (11484)
  covalent geometry    : angle       0.61151 (15534)
  hydrogen bonds       : bond        0.05355 (  510)
  hydrogen bonds       : angle       4.36717 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.8890 (mm) cc_final: 0.8608 (tp)
REVERT: A   77 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6609 (t80)
REVERT: A   95 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5523 (t80)
REVERT: A  257 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7272 (mp)
REVERT: A  350 TRP cc_start: 0.8576 (m-90) cc_final: 0.7976 (m-90)
REVERT: C  398 GLU cc_start: 0.8726 (tp30) cc_final: 0.8477 (tp30)
REVERT: C  401 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7405 (mp10)
  outliers start: 24
  outliers final: 18
  residues processed: 110
  average time/residue: 0.0962
  time to fit residues: 15.5476
Evaluate side-chains
  108 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  343 MET
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  237 TYR
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  311 HIS
Chi-restraints excluded: chain C residue  479 VAL
Chi-restraints excluded: chain C residue  502 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 115 optimal weight:    7.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.2980
   chunk 42 optimal weight:    0.0170
   chunk 69 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 111 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.5820

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS
A 214 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.145414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.111999 restraints weight = 16707.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.42
r_work: 0.3298 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11484  Z= 0.110
  Angle     :  0.541   9.222  15534  Z= 0.284
  Chirality :  0.043   0.195   1786
  Planarity :  0.003   0.038   1965
  Dihedral  :  4.313  40.682   1510
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.81 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.54 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.33 (0.24), residues: 1372
  helix:  1.72 (0.24), residues: 533
  sheet:  0.05 (0.31), residues: 321
  loop : -1.27 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 152 
 TYR   0.023   0.001   TYR A 609 
 PHE   0.021   0.001   PHE C 328 
 TRP   0.019   0.002   TRP A 417 
 HIS   0.004   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11484)
  covalent geometry    : angle       0.54122 (15534)
  hydrogen bonds       : bond        0.03842 (  510)
  hydrogen bonds       : angle       4.13541 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.8869 (mm) cc_final: 0.8584 (tp)
REVERT: A   77 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6463 (t80)
REVERT: A   95 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5048 (t80)
REVERT: A  257 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7283 (mp)
REVERT: A  350 TRP cc_start: 0.8541 (m-90) cc_final: 0.7935 (m-90)
REVERT: B  161 LEU cc_start: 0.8723 (tp) cc_final: 0.8119 (pp)
REVERT: C  152 PHE cc_start: 0.7780 (t80) cc_final: 0.7330 (t80)
REVERT: C  398 GLU cc_start: 0.8651 (tp30) cc_final: 0.8438 (tp30)
REVERT: C  401 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7254 (mp10)
REVERT: C  473 MET cc_start: 0.8576 (ttm) cc_final: 0.8359 (ttp)
  outliers start: 22
  outliers final: 14
  residues processed: 106
  average time/residue: 0.1020
  time to fit residues: 15.3929
Evaluate side-chains
  102 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  237 TYR
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  311 HIS
Chi-restraints excluded: chain C residue  479 VAL
Chi-restraints excluded: chain C residue  502 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 57 optimal weight:    7.9990
   chunk 51 optimal weight:    0.3980
   chunk 43 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 35 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS
A 214 GLN
C 311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.113394 restraints weight = 16921.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 3.35
r_work: 0.3310 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11484  Z= 0.102
  Angle     :  0.518   8.675  15534  Z= 0.271
  Chirality :  0.042   0.176   1786
  Planarity :  0.003   0.038   1965
  Dihedral  :  4.117  39.703   1510
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.10 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.93 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.52 (0.24), residues: 1372
  helix:  1.89 (0.24), residues: 533
  sheet:  0.23 (0.32), residues: 314
  loop : -1.23 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 152 
 TYR   0.026   0.001   TYR A 609 
 PHE   0.024   0.001   PHE C 328 
 TRP   0.021   0.001   TRP A 417 
 HIS   0.004   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (11484)
  covalent geometry    : angle       0.51756 (15534)
  hydrogen bonds       : bond        0.03559 (  510)
  hydrogen bonds       : angle       4.00200 ( 1455)

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

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

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2744 Ramachandran restraints generated.
    1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 ILE cc_start: 0.8794 (mm) cc_final: 0.8508 (tp)
REVERT: A   77 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6463 (t80)
REVERT: A   95 PHE cc_start: 0.6237 (OUTLIER) cc_final: 0.4984 (t80)
REVERT: A  257 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7108 (mp)
REVERT: A  350 TRP cc_start: 0.8551 (m-90) cc_final: 0.7919 (m-90)
REVERT: B    9 GLU cc_start: 0.7047 (pm20) cc_final: 0.6711 (pm20)
REVERT: B  161 LEU cc_start: 0.8675 (tp) cc_final: 0.8062 (pp)
REVERT: C  398 GLU cc_start: 0.8680 (tp30) cc_final: 0.8462 (tp30)
REVERT: C  473 MET cc_start: 0.8540 (ttm) cc_final: 0.8326 (ttp)
  outliers start: 19
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0978
  time to fit residues: 14.7276
Evaluate side-chains
  103 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 HIS
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   77 PHE
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  349 MET
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain B residue   60 THR
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain C residue  237 TYR
Chi-restraints excluded: chain C residue  289 VAL
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  311 HIS
Chi-restraints excluded: chain C residue  479 VAL
Chi-restraints excluded: chain C residue  502 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.146097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.112292 restraints weight = 16924.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.42
r_work: 0.3295 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11484  Z= 0.115
  Angle     :  0.525   8.636  15534  Z= 0.274
  Chirality :  0.043   0.177   1786
  Planarity :  0.003   0.038   1965
  Dihedral  :  4.117  40.067   1510
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.32 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.01 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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 aren not related in a simple way.
  whole:  0.51 (0.24), residues: 1372
  helix:  1.89 (0.24), residues: 533
  sheet:  0.12 (0.31), residues: 328
  loop : -1.19 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 152 
 TYR   0.025   0.001   TYR A 609 
 PHE   0.023   0.001   PHE C 328 
 TRP   0.042   0.002   TRP A 417 
 HIS   0.007   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (11484)
  covalent geometry    : angle       0.52532 (15534)
  hydrogen bonds       : bond        0.03730 (  510)
  hydrogen bonds       : angle       3.99846 ( 1455)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2443.54 seconds
wall clock time: 42 minutes 43.13 seconds (2563.13 seconds total)