Starting phenix.real_space_refine
on Fri Sep 11 23:03:16 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7s4u_24833/09_2026/7s4u_24833.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.107
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     142      5.49       5
     S      16      5.16       5
     C    7078      2.51       5
     N    2093      2.21       5
     O    2598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11927
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1092, 8928
          Classifications: {'peptide': 1092}
          Link IDs: {'PTRANS': 29, 'TRANS': 1062}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 2080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 2080
          Classifications: {'RNAv2': 97}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 48, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 17, 'rna3p': 79}
    Chain: "C"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 648
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "D"
      Number of atoms: 271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 271
          Classifications: {'DNA': 13}
          Link IDs: {'rna3p': 12}
  Time building chain proxies: 2.52, per 1000 atoms: 0.21
  Number of scatterers: 11927
  At special positions: 0
  Unit cell: (89.1, 130.9, 145.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P     142     15.00
     O    2598      8.00
     N    2093      7.00
     C    7078      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: 0.98
  Conformation dependent library (CDL) restraints added in 347.8 milliseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 5 sheets defined
      58.2% alpha, 8.4% beta
      38 base pairs and 76 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 91
      removed outlier: 3.794A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ASN A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.572A  pdb=" N   LEU A 101 " --> pdb=" O   PHE A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 111
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 135 through 144
      removed outlier: 3.612A  pdb=" N   LYS A 141 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.653A  pdb=" N   HIS A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   MET A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 3.547A  pdb=" N   SER A 179 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.597A  pdb=" N   ALA A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 237 through 246
      removed outlier: 4.775A  pdb=" N   ALA A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 262
      removed outlier: 3.697A  pdb=" N   ASP A 261 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 275 through 282
      removed outlier: 3.649A  pdb=" N   GLN A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 306
      removed outlier: 4.112A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASP A 304 " --> pdb=" O   ILE A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.537A  pdb=" N   ILE A 322 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   HIS A 328 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 334 " --> pdb=" O   GLN A 330 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 337 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 351
      removed outlier: 3.722A  pdb=" N   TYR A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LYS A 348 " --> pdb=" O   PRO A 344 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   GLU A 349 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
    Processing helix  chain 'A' and resid 368 through 383
      Proline residue:  A 378  - end of helix
      removed outlier: 3.698A  pdb=" N   MET A 383 " --> pdb=" O   ILE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.278A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLN A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 435
      removed outlier: 4.009A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ASP A 435 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 430 through 435'
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 474 through 478
      removed outlier: 3.567A  pdb=" N   ASN A 477 " --> pdb=" O   THR A 474 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE A 478 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 474 through 478'
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 3.920A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 562 through 573
      removed outlier: 3.514A  pdb=" N   GLU A 566 " --> pdb=" O   LYS A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'A' and resid 609 through 611
      No H-bonds generated for 'chain 'A' and resid 609 through 611'
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 4.188A  pdb=" N   ASP A 618 " --> pdb=" O   ASP A 614 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   THR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.720A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 687 through 691
      removed outlier: 3.524A  pdb=" N   ARG A 691 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 700
      removed outlier: 3.917A  pdb=" N   HIS A 698 " --> pdb=" O   MET A 694 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 710
      removed outlier: 5.729A  pdb=" N   GLU A 706 " --> pdb=" O   LEU A 702 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ASP A 707 " --> pdb=" O   THR A 703 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ILE A 708 " --> pdb=" O   PHE A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 724
    Processing helix  chain 'A' and resid 725 through 727
      No H-bonds generated for 'chain 'A' and resid 725 through 727'
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.850A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   GLY A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.572A  pdb=" N   LYS A 929 " --> pdb=" O   ARG A 925 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 932 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG A 938 " --> pdb=" O   ILE A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.266A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1000
    Processing helix  chain 'A' and resid 1076 through 1089
      removed outlier: 4.189A  pdb=" N   PHE A1080 " --> pdb=" O   LYS A1076 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ALA A1081 " --> pdb=" O   GLY A1077 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   THR A1082 " --> pdb=" O   ARG A1078 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1186
      removed outlier: 3.532A  pdb=" N   GLY A1186 " --> pdb=" O   LEU A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
      removed outlier: 3.585A  pdb=" N   VAL A1233 " --> pdb=" O   PRO A1229 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A1238 " --> pdb=" O   ASN A1234 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A1239 " --> pdb=" O   PHE A1235 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   HIS A1241 " --> pdb=" O   TYR A1237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1260
      removed outlier: 4.191A  pdb=" N   GLN A1254 " --> pdb=" O   GLU A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.883A  pdb=" N   ASN A1308 " --> pdb=" O   GLU A1304 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1338 through 1343
      removed outlier: 3.605A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.397A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TRP A  18 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 3.655A  pdb=" N   LYS A  30 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 10.524A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.550A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1106 through 1111
      removed outlier: 6.938A  pdb=" N   LYS A1107 " --> pdb=" O   PRO A1137 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   SER A1109 " --> pdb=" O   ASP A1135 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   ASP A1135 " --> pdb=" O   SER A1109 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A1133 " --> pdb=" O   LEU A1111 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.667A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326

    385 hydrogen bonds defined for protein.
    1107 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      97 hydrogen bonds
      194 hydrogen bond angles
      0 basepair planarities
      38 basepair parallelities
      76 stacking parallelities
  Total time for adding SS restraints: 2.85

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2410
        1.33 -     1.45: 3417
        1.45 -     1.57: 6303
        1.57 -     1.69: 281
        1.69 -     1.81: 31
  Bond restraints: 12442
  Sorted by residual:
  bond pdb=" C3'  DG C  12 "
       pdb=" C2'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.16e+00
  bond pdb=" C3'  DT C   9 "
       pdb=" C2'  DT C   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.59e+00
  bond pdb=" C5'  DG C  35 "
       pdb=" C4'  DG C  35 "
    ideal  model  delta    sigma   weight residual
    1.512  1.531 -0.019 7.00e-03 2.04e+04 7.75e+00
  bond pdb=" C3'  DC C  17 "
       pdb=" C2'  DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 7.16e+00
  bond pdb=" C3'  DC D  45 "
       pdb=" C2'  DC D  45 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.54e+00
  ... (remaining 12437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 16628
        1.97 -     3.94: 682
        3.94 -     5.91: 89
        5.91 -     7.88: 13
        7.88 -     9.85: 1
  Bond angle restraints: 17413
  Sorted by residual:
  angle pdb=" O4'  DT C  23 "
        pdb=" C4'  DT C  23 "
        pdb=" C3'  DT C  23 "
      ideal   model   delta    sigma   weight residual
     106.00  102.58    3.42 6.00e-01 2.78e+00 3.25e+01
  angle pdb=" C3'   C B  90 "
        pdb=" O3'   C B  90 "
        pdb=" P     G B  91 "
      ideal   model   delta    sigma   weight residual
     119.70  126.48   -6.78 1.20e+00 6.94e-01 3.19e+01
  angle pdb=" C3'   C B   2 "
        pdb=" O3'   C B   2 "
        pdb=" P     G B   3 "
      ideal   model   delta    sigma   weight residual
     119.70  125.75   -6.05 1.20e+00 6.94e-01 2.54e+01
  angle pdb=" O4'  DC C  26 "
        pdb=" C4'  DC C  26 "
        pdb=" C3'  DC C  26 "
      ideal   model   delta    sigma   weight residual
     106.00  103.00    3.00 6.00e-01 2.78e+00 2.50e+01
  angle pdb=" N3   DT C  30 "
        pdb=" C4   DT C  30 "
        pdb=" O4   DT C  30 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.02e+01
  ... (remaining 17408 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.30: 6816
       35.30 -    70.60: 381
       70.60 -   105.90: 31
      105.90 -   141.20: 3
      141.20 -   176.49: 2
  Dihedral angle restraints: 7233
    sinusoidal: 4021
      harmonic: 3212
  Sorted by residual:
  dihedral pdb=" C4'   C B   4 "
           pdb=" C3'   C B   4 "
           pdb=" C2'   C B   4 "
           pdb=" C1'   C B   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -39.00   75.34     1      3.10e+00 1.04e-01 7.46e+02
  dihedral pdb=" C4'   A B   5 "
           pdb=" C3'   A B   5 "
           pdb=" C2'   A B   5 "
           pdb=" C1'   A B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -37.62   73.97     1      3.10e+00 1.04e-01 7.23e+02
  dihedral pdb=" C4'   C B  54 "
           pdb=" C3'   C B  54 "
           pdb=" C2'   C B  54 "
           pdb=" C1'   C B  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.45   73.79     1      3.10e+00 1.04e-01 7.20e+02
  ... (remaining 7230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1750
       0.080 -    0.160: 139
       0.160 -    0.240: 79
       0.240 -    0.321: 51
       0.321 -    0.401: 3
  Chirality restraints: 2022
  Sorted by residual:
  chirality pdb=" P     G B   3 "
            pdb=" OP1   G B   3 "
            pdb=" OP2   G B   3 "
            pdb=" O5'   G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.57   -0.40 2.00e-01 2.50e+01 4.01e+00
  chirality pdb=" P     G B  91 "
            pdb=" OP1   G B  91 "
            pdb=" OP2   G B  91 "
            pdb=" O5'   G B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.54   -0.36 2.00e-01 2.50e+01 3.29e+00
  chirality pdb=" C2'   A B   5 "
            pdb=" C3'   A B   5 "
            pdb=" O2'   A B   5 "
            pdb=" C1'   A B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.45   -0.34 2.00e-01 2.50e+01 2.81e+00
  ... (remaining 2019 not shown)

  Planarity restraints: 1694
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   3 "   -0.036 2.00e-02 2.50e+03   1.61e-02 7.78e+00
        pdb=" N9    G B   3 "    0.040 2.00e-02 2.50e+03
        pdb=" C8    G B   3 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G B   3 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B   3 "   -0.008 2.00e-02 2.50e+03
        pdb=" O6    G B   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G B   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G B   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B   3 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    G B   3 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.028 2.00e-02 2.50e+03   1.30e-02 4.66e+00
        pdb=" N9    A B   7 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG C  35 "    0.028 2.00e-02 2.50e+03   1.18e-02 4.16e+00
        pdb=" N9   DG C  35 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8   DG C  35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG C  35 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG C  35 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG C  35 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DG C  35 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG C  35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG C  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG C  35 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DG C  35 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1691 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 251
        2.65 -     3.21: 10971
        3.21 -     3.78: 18440
        3.78 -     4.34: 25014
        4.34 -     4.90: 38258
  Nonbonded interactions: 92934
  Sorted by model distance:
  nonbonded pdb=" O2'   C B  90 "
            pdb=" OP1   G B  91 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" OG  SER A 541 "
            pdb=" OD2 ASP A 686 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OD1 ASN A  14 "
            pdb=" OG  SER A  55 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" OH  TYR A 373 "
            pdb=" O   LEU A 398 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O2'   A B  37 "
            pdb=" OP1   G B  38 "
     model   vdw
     2.200 3.040
  ... (remaining 92929 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=0.00 max=1.00 mean=0.92
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.890
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.540
  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:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12442  Z= 0.284
  Angle     :  0.864   9.851  17413  Z= 0.505
  Chirality :  0.075   0.401   2022
  Planarity :  0.004   0.042   1694
  Dihedral  : 18.795 176.495   5147
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.09 (0.25), residues: 1076
  helix: -0.75 (0.22), residues: 517
  sheet: -0.15 (0.52), residues: 106
  loop : -0.61 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 664 
 TYR   0.026   0.002   TYR A 362 
 PHE   0.025   0.002   PHE A 478 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.007   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.28 (12442)
  covalent geometry    : angle       0.86376 /  0.50 (17413)
  hydrogen bonds       : bond        0.16339 / 10.62 (  482)
  hydrogen bonds       : angle       6.30250 /  4.48 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.275 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1290
  time to fit residues: 14.6579
Evaluate side-chains
  47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.133880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.102417 restraints weight = 23054.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.105182 restraints weight = 47296.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.105068 restraints weight = 21686.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.105463 restraints weight = 17942.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.105843 restraints weight = 14597.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12442  Z= 0.235
  Angle     :  1.180  21.409  17413  Z= 0.519
  Chirality :  0.108   1.352   2022
  Planarity :  0.004   0.038   1694
  Dihedral  : 19.497 173.112   2831
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.78 %
    Favored  : 95.61 %
  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: -1.03 (0.25), residues: 1076
  helix: -0.58 (0.22), residues: 528
  sheet: -0.19 (0.54), residues: 104
  loop : -0.73 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1303 
 TYR   0.027   0.002   TYR A   5 
 PHE   0.026   0.002   PHE A 704 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.006   0.002   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00480 /  0.24 (12442)
  covalent geometry    : angle       1.18027 /  0.52 (17413)
  hydrogen bonds       : bond        0.06661 /  4.20 (  482)
  hydrogen bonds       : angle       5.01848 /  3.55 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 58
  average time/residue: 0.1345
  time to fit residues: 10.6887
Evaluate side-chains
  47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  950 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 98 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0670
   overall best weight:    0.5918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.135790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.103554 restraints weight = 23287.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.106832 restraints weight = 49724.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.107124 restraints weight = 21376.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.107398 restraints weight = 16421.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.110334 restraints weight = 14617.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12442  Z= 0.165
  Angle     :  0.917  17.780  17413  Z= 0.410
  Chirality :  0.078   1.109   2022
  Planarity :  0.004   0.036   1694
  Dihedral  : 19.570 171.914   2831
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  4.39 %
    Favored  : 94.80 %
  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: -0.76 (0.25), residues: 1076
  helix: -0.28 (0.22), residues: 530
  sheet: -0.22 (0.53), residues: 106
  loop : -0.66 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1303 
 TYR   0.023   0.002   TYR A 325 
 PHE   0.026   0.001   PHE A 704 
 TRP   0.014   0.002   TRP A  18 
 HIS   0.006   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.16 (12442)
  covalent geometry    : angle       0.91706 /  0.41 (17413)
  hydrogen bonds       : bond        0.05309 /  3.35 (  482)
  hydrogen bonds       : angle       4.58215 /  3.26 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  661 ARG cc_start: 0.8301 (mmm160) cc_final: 0.8098 (mmp80)
  outliers start: 8
  outliers final: 4
  residues processed: 56
  average time/residue: 0.1286
  time to fit residues: 10.2885
Evaluate side-chains
  47 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 110 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 117 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.133365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.102941 restraints weight = 23201.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.105264 restraints weight = 48482.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.104735 restraints weight = 21084.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.105956 restraints weight = 17104.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.105845 restraints weight = 13812.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12442  Z= 0.204
  Angle     :  0.907  13.051  17413  Z= 0.409
  Chirality :  0.074   1.067   2022
  Planarity :  0.004   0.039   1694
  Dihedral  : 19.474 169.669   2831
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  5.82 %
    Favored  : 93.16 %
  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: -1.01 (0.25), residues: 1076
  helix: -0.40 (0.22), residues: 539
  sheet: -0.49 (0.53), residues: 106
  loop : -0.89 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1298 
 TYR   0.027   0.002   TYR A 362 
 PHE   0.021   0.002   PHE A 704 
 TRP   0.013   0.002   TRP A  18 
 HIS   0.008   0.002   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.20 (12442)
  covalent geometry    : angle       0.90723 /  0.41 (17413)
  hydrogen bonds       : bond        0.06238 /  3.95 (  482)
  hydrogen bonds       : angle       4.62495 /  3.29 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  751 MET cc_start: 0.7636 (tpp) cc_final: 0.7347 (tpp)
  outliers start: 10
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1036
  time to fit residues: 8.4880
Evaluate side-chains
  52 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  986 ASP
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 83 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 119 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 110 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0870
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.8280

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 ASN
** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 726 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.134560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.102773 restraints weight = 23144.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.104493 restraints weight = 52258.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.105528 restraints weight = 24456.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.106018 restraints weight = 17702.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.106519 restraints weight = 15827.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12442  Z= 0.161
  Angle     :  0.843  12.429  17413  Z= 0.380
  Chirality :  0.068   0.819   2022
  Planarity :  0.004   0.037   1694
  Dihedral  : 19.382 170.134   2831
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  7.14 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.25), residues: 1076
  helix: -0.23 (0.22), residues: 538
  sheet: -0.54 (0.52), residues: 108
  loop : -0.80 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1298 
 TYR   0.022   0.002   TYR A 325 
 PHE   0.013   0.001   PHE A 704 
 TRP   0.013   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.16 (12442)
  covalent geometry    : angle       0.84285 /  0.38 (17413)
  hydrogen bonds       : bond        0.05390 /  3.41 (  482)
  hydrogen bonds       : angle       4.43635 /  3.16 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8045 (mmt) cc_final: 0.7667 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 57
  average time/residue: 0.1028
  time to fit residues: 8.5370
Evaluate side-chains
  49 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0170
   chunk 91 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.9220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 402 GLN
A 726 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.134031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.102884 restraints weight = 23237.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.105891 restraints weight = 50733.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.105914 restraints weight = 20351.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.106880 restraints weight = 16452.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107073 restraints weight = 13731.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12442  Z= 0.170
  Angle     :  0.846  11.839  17413  Z= 0.381
  Chirality :  0.067   0.683   2022
  Planarity :  0.004   0.042   1694
  Dihedral  : 19.337 173.895   2831
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  8.37 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.25), residues: 1076
  helix: -0.08 (0.23), residues: 527
  sheet: -0.60 (0.52), residues: 107
  loop : -0.81 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1298 
 TYR   0.022   0.002   TYR A 362 
 PHE   0.014   0.001   PHE A1324 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.005   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.17 (12442)
  covalent geometry    : angle       0.84627 /  0.38 (17413)
  hydrogen bonds       : bond        0.05616 /  3.56 (  482)
  hydrogen bonds       : angle       4.45633 /  3.17 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1207
  time to fit residues: 9.9081
Evaluate side-chains
  53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 49 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 46 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.134501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.104154 restraints weight = 23089.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.107161 restraints weight = 50559.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.106807 restraints weight = 20982.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.108070 restraints weight = 16786.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.108089 restraints weight = 13311.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12442  Z= 0.158
  Angle     :  0.821  11.191  17413  Z= 0.368
  Chirality :  0.065   0.644   2022
  Planarity :  0.003   0.033   1694
  Dihedral  : 19.292 177.926   2831
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.08 %
    Favored  : 89.69 %
  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: -0.65 (0.25), residues: 1076
  helix:  0.05 (0.23), residues: 524
  sheet: -0.59 (0.51), residues: 107
  loop : -0.82 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1298 
 TYR   0.020   0.001   TYR A 325 
 PHE   0.014   0.001   PHE A 704 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 137 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 (12442)
  covalent geometry    : angle       0.82074 /  0.37 (17413)
  hydrogen bonds       : bond        0.05226 /  3.31 (  482)
  hydrogen bonds       : angle       4.37497 /  3.11 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.7975 (mmt) cc_final: 0.7621 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 57
  average time/residue: 0.1208
  time to fit residues: 10.2502
Evaluate side-chains
  53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 35 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 85 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.134510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.102747 restraints weight = 23028.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.104833 restraints weight = 51755.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.105658 restraints weight = 24137.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.106408 restraints weight = 17567.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.106717 restraints weight = 15711.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12442  Z= 0.157
  Angle     :  0.820  11.129  17413  Z= 0.368
  Chirality :  0.065   0.634   2022
  Planarity :  0.003   0.034   1694
  Dihedral  : 19.275 179.465   2831
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.08 %
    Favored  : 89.59 %
  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: -0.67 (0.26), residues: 1076
  helix:  0.05 (0.23), residues: 530
  sheet: -0.60 (0.51), residues: 107
  loop : -0.87 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1298 
 TYR   0.020   0.001   TYR A 325 
 PHE   0.013   0.001   PHE A1324 
 TRP   0.011   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.16 (12442)
  covalent geometry    : angle       0.82027 /  0.37 (17413)
  hydrogen bonds       : bond        0.05251 /  3.33 (  482)
  hydrogen bonds       : angle       4.36250 /  3.11 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.7925 (mmt) cc_final: 0.7566 (mmm)
REVERT: A  661 ARG cc_start: 0.8250 (mmm160) cc_final: 0.8033 (mmp80)
  outliers start: 13
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1156
  time to fit residues: 9.6777
Evaluate side-chains
  55 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  616 LEU
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.134755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.104849 restraints weight = 23122.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.107439 restraints weight = 49480.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.107048 restraints weight = 21459.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108160 restraints weight = 16880.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.108214 restraints weight = 13622.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12442  Z= 0.152
  Angle     :  0.812  11.024  17413  Z= 0.366
  Chirality :  0.064   0.630   2022
  Planarity :  0.003   0.034   1694
  Dihedral  : 19.259 179.193   2831
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.69 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.26), residues: 1076
  helix:  0.10 (0.23), residues: 529
  sheet: -0.58 (0.51), residues: 107
  loop : -0.88 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1298 
 TYR   0.020   0.001   TYR A 325 
 PHE   0.030   0.001   PHE A 196 
 TRP   0.011   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 (12442)
  covalent geometry    : angle       0.81237 /  0.37 (17413)
  hydrogen bonds       : bond        0.05104 /  3.24 (  482)
  hydrogen bonds       : angle       4.30787 /  3.06 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.7966 (mmt) cc_final: 0.7609 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1153
  time to fit residues: 9.4654
Evaluate side-chains
  53 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 30 optimal weight:    0.1980
   chunk 68 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  46 ASN
A 726 ASN
A 983 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.131220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.100322 restraints weight = 23294.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.103125 restraints weight = 51419.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.103051 restraints weight = 21419.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.103960 restraints weight = 16903.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.104146 restraints weight = 14195.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  12442  Z= 0.293
  Angle     :  0.964  12.179  17413  Z= 0.438
  Chirality :  0.071   0.605   2022
  Planarity :  0.005   0.043   1694
  Dihedral  : 19.446 179.247   2831
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.10 %
    Favored  : 89.29 %
  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: -1.04 (0.25), residues: 1076
  helix: -0.18 (0.23), residues: 523
  sheet: -1.02 (0.50), residues: 106
  loop : -1.08 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 403 
 TYR   0.032   0.002   TYR A 362 
 PHE   0.026   0.002   PHE A 196 
 TRP   0.008   0.002   TRP A  18 
 HIS   0.008   0.002   HIS A 160 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00659 /  0.29 (12442)
  covalent geometry    : angle       0.96366 /  0.44 (17413)
  hydrogen bonds       : bond        0.07527 /  4.78 (  482)
  hydrogen bonds       : angle       4.76538 /  3.39 ( 1301)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.7483 (tpp) cc_final: 0.7027 (tpp)
  outliers start: 6
  outliers final: 6
  residues processed: 55
  average time/residue: 0.1160
  time to fit residues: 9.3492
Evaluate side-chains
  55 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  992 VAL
Chi-restraints excluded: chain A residue 1092 VAL
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1254 GLN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 90 optimal weight:    0.5980
   chunk 112 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 95 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 102 optimal weight:    0.8980
   chunk 119 optimal weight:    9.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 726 ASN
A 983 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.133984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.105305 restraints weight = 23319.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.106777 restraints weight = 51131.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106952 restraints weight = 21782.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.107917 restraints weight = 17052.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.107974 restraints weight = 13745.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12442  Z= 0.159
  Angle     :  0.836  11.093  17413  Z= 0.377
  Chirality :  0.065   0.617   2022
  Planarity :  0.004   0.049   1694
  Dihedral  : 19.348 176.907   2831
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.31 %
    Favored  : 88.98 %
  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: -0.76 (0.26), residues: 1076
  helix:  0.07 (0.23), residues: 521
  sheet: -0.85 (0.50), residues: 106
  loop : -0.98 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1298 
 TYR   0.022   0.002   TYR A 362 
 PHE   0.028   0.001   PHE A 196 
 TRP   0.012   0.002   TRP A  18 
 HIS   0.004   0.001   HIS A1349 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.16 (12442)
  covalent geometry    : angle       0.83554 /  0.38 (17413)
  hydrogen bonds       : bond        0.05474 /  3.44 (  482)
  hydrogen bonds       : angle       4.43296 /  3.16 ( 1301)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1532.75 seconds
wall clock time: 27 minutes 41.10 seconds (1661.10 seconds total)