Starting phenix.real_space_refine
on Mon Jul 28 23:22:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ci5_16670/07_2025/8ci5_16670.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002
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      11      5.49       5
     S      49      5.16       5
     C    6629      2.51       5
     N    1738      2.21       5
     O    1938      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10365
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10128
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1258, 10124
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 41, 'TRANS': 1216}
          Chain breaks: 15
      Conformer: "B"
        Number of residues, atoms: 1258, 10124
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 41, 'TRANS': 1216}
          Chain breaks: 15
          bond proxies already assigned to first conformer: 10337
    Chain: "C"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 237
          Classifications: {'RNA': 11}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 8}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY A1047 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A1047 " occ=0.50
  Time building chain proxies: 11.68, per 1000 atoms: 1.13
  Number of scatterers: 10365
  At special positions: 0
  Unit cell: (101.15, 88.4, 125.8, 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      49     16.00
     P      11     15.00
     O    1938      8.00
     N    1738      7.00
     C    6629      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: 2.64
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2388

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 12 sheets defined
      57.1% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.760A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 277
      removed outlier: 3.961A  pdb=" N   VAL A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 282
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 328 through 343
    Processing helix  chain 'A' and resid 345 through 353
      removed outlier: 3.821A  pdb=" N   ILE A 350 " --> pdb=" O   ARG A 346 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN A 351 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR A 353 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 378
      removed outlier: 4.031A  pdb=" N   LEU A 378 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
      removed outlier: 3.694A  pdb=" N   LYS A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 426
    Processing helix  chain 'A' and resid 451 through 464
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 471 through 491
      removed outlier: 3.690A  pdb=" N   HIS A 475 " --> pdb=" O   THR A 471 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP A 482 " --> pdb=" O   HIS A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 573
    Processing helix  chain 'A' and resid 573 through 594
    Processing helix  chain 'A' and resid 598 through 616
      removed outlier: 3.681A  pdb=" N   GLN A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 635
      removed outlier: 3.587A  pdb=" N   CYS A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A 623 " --> pdb=" O   LYS A 619 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR A 629 " --> pdb=" O   ASP A 625 " (cutoff:3.500A)
      Proline residue:  A 632  - end of helix
      removed outlier: 3.611A  pdb=" N   THR A 635 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 649
      removed outlier: 3.667A  pdb=" N   PHE A 649 " --> pdb=" O   ILE A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 675
      removed outlier: 3.754A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 655 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN A 675 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 727
      removed outlier: 4.347A  pdb=" N   LEU A 717 " --> pdb=" O   HIS A 713 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 742 through 761
      removed outlier: 4.583A  pdb=" N   THR A 746 " --> pdb=" O   ILE A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 768
      removed outlier: 3.523A  pdb=" N   MET A 765 " --> pdb=" O   GLY A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 777
    Processing helix  chain 'A' and resid 787 through 803
    Processing helix  chain 'A' and resid 805 through 815
      removed outlier: 3.579A  pdb=" N   MET A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A 815 " --> pdb=" O   SER A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 830
      removed outlier: 3.923A  pdb=" N   SER A 830 " --> pdb=" O   ARG A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 848 through 861
      removed outlier: 3.567A  pdb=" N   ASN A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG A 859 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   GLN A 861 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 873
    Processing helix  chain 'A' and resid 899 through 918
    Processing helix  chain 'A' and resid 932 through 947
      removed outlier: 3.661A  pdb=" N   ALA A 947 " --> pdb=" O   ALA A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 992
      removed outlier: 4.451A  pdb=" N   ARG A 988 " --> pdb=" O   ALA A 984 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA A 992 " --> pdb=" O   ARG A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1011
    Processing helix  chain 'A' and resid 1021 through 1030
      removed outlier: 3.515A  pdb=" N   ASP A1029 " --> pdb=" O   HIS A1025 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1045
      removed outlier: 3.611A  pdb=" N   ASP A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE A1041 " --> pdb=" O   ALA A1037 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE A1045 " --> pdb=" O   PHE A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1062 through 1083
    Processing helix  chain 'A' and resid 1115 through 1127
      removed outlier: 3.668A  pdb=" N   ALA A1127 " --> pdb=" O   GLN A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1135
      removed outlier: 3.642A  pdb=" N   ALA A1134 " --> pdb=" O   HIS A1131 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A1135 " --> pdb=" O   TRP A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1154
    Processing helix  chain 'A' and resid 1186 through 1192
      removed outlier: 3.521A  pdb=" N   LEU A1190 " --> pdb=" O   PHE A1186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1219
      removed outlier: 3.654A  pdb=" N   ASP A1205 " --> pdb=" O   GLY A1201 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   CYS A1213 " --> pdb=" O   ALA A1209 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A1219 " --> pdb=" O   LYS A1215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1242
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1283 through 1301
      removed outlier: 3.905A  pdb=" N   LYS A1287 " --> pdb=" O   GLY A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1303 through 1318
      removed outlier: 3.617A  pdb=" N   LEU A1318 " --> pdb=" O   PHE A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1355 through 1366
    Processing helix  chain 'A' and resid 1367 through 1371
      removed outlier: 3.707A  pdb=" N   ASP A1370 " --> pdb=" O   PRO A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1376 through 1390
      removed outlier: 3.534A  pdb=" N   LEU A1380 " --> pdb=" O   GLY A1376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1390 through 1398
    Processing helix  chain 'A' and resid 1401 through 1408
      removed outlier: 4.240A  pdb=" N   LEU A1405 " --> pdb=" O   SER A1401 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ARG A1406 " --> pdb=" O   PRO A1402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1440
    Processing helix  chain 'A' and resid 1449 through 1456
    Processing helix  chain 'A' and resid 1504 through 1513
      removed outlier: 4.239A  pdb=" N   TYR A1512 " --> pdb=" O   ILE A1508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1525
    Processing helix  chain 'A' and resid 1531 through 1547
      removed outlier: 4.108A  pdb=" N   GLN A1537 " --> pdb=" O   SER A1533 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU A1546 " --> pdb=" O   GLY A1542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 4.200A  pdb=" N   LEU A1557 " --> pdb=" O   LEU A1553 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS A1558 " --> pdb=" O   PRO A1554 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1553 through 1558'
    Processing helix  chain 'A' and resid 1560 through 1567
      removed outlier: 3.534A  pdb=" N   LEU A1564 " --> pdb=" O   ILE A1560 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA A1567 " --> pdb=" O   LEU A1563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1582 through 1593
      removed outlier: 3.774A  pdb=" N   SER A1588 " --> pdb=" O   GLU A1584 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR A1589 " --> pdb=" O   SER A1585 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261
      removed outlier: 3.700A  pdb=" N   THR A1164 " --> pdb=" O   SER A 971 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR A1105 " --> pdb=" O   MET A 968 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA A1101 " --> pdb=" O   ALA A 972 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A1106 " --> pdb=" O   PHE A1091 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 284
      removed outlier: 5.830A  pdb=" N   LYS A 283 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298
      removed outlier: 4.158A  pdb=" N   ILE A 536 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 504
      removed outlier: 5.174A  pdb=" N   THR A 530 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A 553 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 504
      removed outlier: 3.570A  pdb=" N   ILE A 563 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703
    Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 898
      removed outlier: 7.082A  pdb=" N   ALA A 880 " --> pdb=" O   PHE A1019 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 954
    Processing sheet with id=AA9, first strand: chain 'A' and resid 964 through 965
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1170 through 1172
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1418 through 1420
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1491

    508 hydrogen bonds defined for protein.
    1443 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: 4.08

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2288
        1.33 -     1.45: 2508
        1.45 -     1.57: 5715
        1.57 -     1.69: 22
        1.69 -     1.81: 79
  Bond restraints: 10612
  Sorted by residual:
  bond pdb=" CA  SER A1193 "
       pdb=" C   SER A1193 "
    ideal  model  delta    sigma   weight residual
    1.522  1.462  0.061 1.34e-02 5.57e+03 2.04e+01
  bond pdb=" C   ILE A1264 "
       pdb=" N   PRO A1265 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.030 9.80e-03 1.04e+04 9.14e+00
  bond pdb=" N   GLN A1059 "
       pdb=" CA  GLN A1059 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.03e+00
  bond pdb=" C   ALA A 845 "
       pdb=" N   ALA A 846 "
    ideal  model  delta    sigma   weight residual
    1.334  1.294  0.040 1.52e-02 4.33e+03 6.89e+00
  bond pdb=" CA  LEU A 464 "
       pdb=" C   LEU A 464 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 7.00e-03 2.04e+04 6.89e+00
  ... (remaining 10607 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 13734
        2.56 -     5.13: 572
        5.13 -     7.69: 66
        7.69 -    10.26: 9
       10.26 -    12.82: 5
  Bond angle restraints: 14386
  Sorted by residual:
  angle pdb=" CA  PRO A1391 "
        pdb=" N   PRO A1391 "
        pdb=" CD  PRO A1391 "
      ideal   model   delta    sigma   weight residual
     112.00  100.12   11.88 1.40e+00 5.10e-01 7.20e+01
  angle pdb=" N   VAL A1049 "
        pdb=" CA  VAL A1049 "
        pdb=" C   VAL A1049 "
      ideal   model   delta    sigma   weight residual
     113.47  106.24    7.23 1.01e+00 9.80e-01 5.13e+01
  angle pdb=" N   VAL A 277 "
        pdb=" CA  VAL A 277 "
        pdb=" C   VAL A 277 "
      ideal   model   delta    sigma   weight residual
     111.77  105.89    5.88 1.04e+00 9.25e-01 3.19e+01
  angle pdb=" C   SER A1531 "
        pdb=" N   LEU A1532 "
        pdb=" CA  LEU A1532 "
      ideal   model   delta    sigma   weight residual
     120.44  126.63   -6.19 1.30e+00 5.92e-01 2.27e+01
  angle pdb=" N   VAL A1252 "
        pdb=" CA  VAL A1252 "
        pdb=" C   VAL A1252 "
      ideal   model   delta    sigma   weight residual
     113.07  106.88    6.19 1.37e+00 5.33e-01 2.04e+01
  ... (remaining 14381 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.94: 6034
       26.94 -    53.87: 266
       53.87 -    80.81: 41
       80.81 -   107.75: 6
      107.75 -   134.68: 1
  Dihedral angle restraints: 6348
    sinusoidal: 2658
      harmonic: 3690
  Sorted by residual:
  dihedral pdb=" O4'   U C   7 "
           pdb=" C1'   U C   7 "
           pdb=" N1    U C   7 "
           pdb=" C2    U C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   65.32  134.68     1      1.50e+01 4.44e-03 7.27e+01
  dihedral pdb=" CA  SER A 926 "
           pdb=" C   SER A 926 "
           pdb=" N   TYR A 927 "
           pdb=" CA  TYR A 927 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.12  -29.88     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  ARG A 893 "
           pdb=" C   ARG A 893 "
           pdb=" N   GLY A 894 "
           pdb=" CA  GLY A 894 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.88  -26.12     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 6345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1262
       0.078 -    0.157: 312
       0.157 -    0.235: 33
       0.235 -    0.314: 2
       0.314 -    0.392: 2
  Chirality restraints: 1611
  Sorted by residual:
  chirality pdb=" CB  VAL A1135 "
            pdb=" CA  VAL A1135 "
            pdb=" CG1 VAL A1135 "
            pdb=" CG2 VAL A1135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CA  PRO A1391 "
            pdb=" N   PRO A1391 "
            pdb=" C   PRO A1391 "
            pdb=" CB  PRO A1391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CB  VAL A1394 "
            pdb=" CA  VAL A1394 "
            pdb=" CG1 VAL A1394 "
            pdb=" CG2 VAL A1394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1608 not shown)

  Planarity restraints: 1772
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1292 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   GLN A1292 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLN A1292 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ALA A1293 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1390 "   -0.053 5.00e-02 4.00e+02   7.30e-02 8.53e+00
        pdb=" N   PRO A1391 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A1391 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A1391 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1297 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.22e+00
        pdb=" C   TYR A1297 "    0.050 2.00e-02 2.50e+03
        pdb=" O   TYR A1297 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A1298 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1769 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1227
        2.73 -     3.27: 9735
        3.27 -     3.82: 16550
        3.82 -     4.36: 20800
        4.36 -     4.90: 35442
  Nonbonded interactions: 83754
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 408 "
            pdb=" NE2 GLN A 414 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE2 GLU A 739 "
            pdb=" OG  SER A1021 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   GLU A1580 "
            pdb=" OG  SER A1585 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR A 913 "
            pdb=" OG1 THR A 990 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   LEU A1119 "
            pdb=" OG  SER A1122 "
     model   vdw
     2.242 3.040
  ... (remaining 83749 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=0.50 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:             6.380
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     34.860
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.070
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
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      :  0.014   0.116  10612  Z= 0.586
  Angle     :  1.190  12.820  14386  Z= 0.665
  Chirality :  0.067   0.392   1611
  Planarity :  0.008   0.073   1772
  Dihedral  : 15.440 134.683   3960
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  8.32 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.88 (0.20), residues: 1229
  helix: -2.14 (0.16), residues: 658
  sheet: -2.93 (0.44), residues: 105
  loop : -2.94 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP A1424 
 HIS   0.011   0.003   HIS A 733 
 PHE   0.048   0.005   PHE A1437 
 TYR   0.039   0.004   TYR A 504 
 ARG   0.029   0.002   ARG A1239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17699 (  498)
  hydrogen bonds       : angle       6.88475 ( 1443)
  covalent geometry    : bond        0.01401 (10612)
  covalent geometry    : angle       1.18965 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  345 ASN cc_start: 0.7830 (t0) cc_final: 0.7598 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2806
  time to fit residues: 46.6658
Evaluate side-chains
  101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.0970
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 331 GLN
A 478 HIS
A 626 ASN
** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1059 GLN
A1126 GLN
A1379 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099959 restraints weight = 15997.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.74
r_work: 0.3100 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10612  Z= 0.130
  Angle     :  0.569   7.940  14386  Z= 0.305
  Chirality :  0.041   0.164   1611
  Planarity :  0.005   0.057   1772
  Dihedral  :  9.119 133.466   1522
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.57 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.78 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.22), residues: 1229
  helix: -0.29 (0.19), residues: 658
  sheet: -1.99 (0.48), residues: 105
  loop : -2.29 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 474 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.025   0.002   PHE A1186 
 TYR   0.016   0.001   TYR A 504 
 ARG   0.003   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05073 (  498)
  hydrogen bonds       : angle       4.79914 ( 1443)
  covalent geometry    : bond        0.00282 (10612)
  covalent geometry    : angle       0.56873 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 1.237 
Fit side-chains
REVERT: A  561 MET cc_start: 0.8370 (mmt) cc_final: 0.8142 (mmm)
REVERT: A  893 ARG cc_start: 0.6696 (ttt-90) cc_final: 0.6286 (tpp80)
REVERT: A 1120 TYR cc_start: 0.7820 (t80) cc_final: 0.7446 (t80)
REVERT: A 1239 ARG cc_start: 0.7841 (ptp-110) cc_final: 0.7628 (ttp80)
  outliers start: 2
  outliers final: 1
  residues processed: 125
  average time/residue: 0.3274
  time to fit residues: 56.1731
Evaluate side-chains
  109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1133 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    0.1980
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.124211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099451 restraints weight = 16352.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.76
r_work: 0.3083 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10612  Z= 0.130
  Angle     :  0.526   7.586  14386  Z= 0.277
  Chirality :  0.040   0.167   1611
  Planarity :  0.004   0.059   1772
  Dihedral  :  8.699 133.535   1522
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.81 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  6.12 %
    Favored  : 93.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.23), residues: 1229
  helix:  0.54 (0.20), residues: 660
  sheet: -1.54 (0.49), residues: 105
  loop : -1.99 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 733 
 PHE   0.022   0.002   PHE A1186 
 TYR   0.013   0.001   TYR A 504 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 (  498)
  hydrogen bonds       : angle       4.46673 ( 1443)
  covalent geometry    : bond        0.00292 (10612)
  covalent geometry    : angle       0.52631 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 1.101 
Fit side-chains
REVERT: A 1120 TYR cc_start: 0.7836 (t80) cc_final: 0.7470 (t80)
  outliers start: 4
  outliers final: 3
  residues processed: 116
  average time/residue: 0.2795
  time to fit residues: 44.3353
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1539 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0570
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.6902

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.125275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.100952 restraints weight = 16085.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.74
r_work: 0.3109 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10612  Z= 0.124
  Angle     :  0.510   7.313  14386  Z= 0.267
  Chirality :  0.040   0.155   1611
  Planarity :  0.004   0.062   1772
  Dihedral  :  8.566 132.539   1522
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.00 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  7.55 %
    Favored  : 91.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.23), residues: 1229
  helix:  0.95 (0.20), residues: 661
  sheet: -1.31 (0.50), residues: 105
  loop : -1.80 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 733 
 PHE   0.020   0.002   PHE A1186 
 TYR   0.011   0.001   TYR A 504 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04471 (  498)
  hydrogen bonds       : angle       4.30653 ( 1443)
  covalent geometry    : bond        0.00279 (10612)
  covalent geometry    : angle       0.51015 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.145 
Fit side-chains
REVERT: A 1120 TYR cc_start: 0.7824 (t80) cc_final: 0.7429 (t80)
REVERT: A 1173 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5573 (pp)
REVERT: A 1451 PHE cc_start: 0.7282 (m-10) cc_final: 0.7072 (m-10)
REVERT: A 1559 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7832 (mmt90)
  outliers start: 7
  outliers final: 3
  residues processed: 122
  average time/residue: 0.3403
  time to fit residues: 56.3597
Evaluate side-chains
  112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 7 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0670
   chunk 11 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 119 optimal weight:    5.9990
   overall best weight:    0.4276

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.102738 restraints weight = 16033.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.75
r_work: 0.3148 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10612  Z= 0.101
  Angle     :  0.485   8.725  14386  Z= 0.251
  Chirality :  0.039   0.168   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.470 132.813   1522
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.00 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.45 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1229
  helix:  1.32 (0.20), residues: 657
  sheet: -0.98 (0.50), residues: 99
  loop : -1.60 (0.26), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.022   0.001   TYR A 927 
 ARG   0.002   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  498)
  hydrogen bonds       : angle       4.13014 ( 1443)
  covalent geometry    : bond        0.00217 (10612)
  covalent geometry    : angle       0.48470 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 1.255 
Fit side-chains
REVERT: A  893 ARG cc_start: 0.6586 (ttt-90) cc_final: 0.6268 (ttt-90)
REVERT: A 1173 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5630 (pp)
REVERT: A 1489 ARG cc_start: 0.7872 (mmt-90) cc_final: 0.7445 (mmt180)
  outliers start: 10
  outliers final: 6
  residues processed: 126
  average time/residue: 0.4986
  time to fit residues: 88.2143
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0270
   chunk 55 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 93 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6238

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.101880 restraints weight = 16083.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.74
r_work: 0.3135 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10612  Z= 0.116
  Angle     :  0.505   8.178  14386  Z= 0.260
  Chirality :  0.040   0.173   1611
  Planarity :  0.004   0.061   1772
  Dihedral  :  8.447 131.873   1522
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.16 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.99 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.24), residues: 1229
  helix:  1.33 (0.20), residues: 665
  sheet: -0.88 (0.51), residues: 99
  loop : -1.50 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 733 
 PHE   0.020   0.002   PHE A1186 
 TYR   0.020   0.001   TYR A 927 
 ARG   0.003   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  498)
  hydrogen bonds       : angle       4.14015 ( 1443)
  covalent geometry    : bond        0.00259 (10612)
  covalent geometry    : angle       0.50475 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A 1120 TYR cc_start: 0.7897 (t80) cc_final: 0.7574 (t80)
REVERT: A 1173 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5640 (pp)
REVERT: A 1489 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7666 (mmt-90)
  outliers start: 9
  outliers final: 7
  residues processed: 123
  average time/residue: 0.3123
  time to fit residues: 52.5865
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0870
   chunk 84 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A1059 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.101317 restraints weight = 16335.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.79
r_work: 0.3120 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10612  Z= 0.108
  Angle     :  0.509  11.100  14386  Z= 0.260
  Chirality :  0.039   0.173   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.407 131.296   1522
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.67 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  9.26 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.24), residues: 1229
  helix:  1.44 (0.20), residues: 665
  sheet: -0.81 (0.51), residues: 99
  loop : -1.43 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.017   0.001   TYR A 927 
 ARG   0.005   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  498)
  hydrogen bonds       : angle       4.07849 ( 1443)
  covalent geometry    : bond        0.00240 (10612)
  covalent geometry    : angle       0.50888 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
REVERT: A 1120 TYR cc_start: 0.7927 (t80) cc_final: 0.7665 (t80)
REVERT: A 1173 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5655 (pp)
REVERT: A 1508 ILE cc_start: 0.8290 (mt) cc_final: 0.8011 (mm)
REVERT: A 1555 GLU cc_start: 0.7742 (mp0) cc_final: 0.6653 (tt0)
REVERT: A 1572 VAL cc_start: 0.8170 (t) cc_final: 0.7810 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 124
  average time/residue: 0.2909
  time to fit residues: 48.9633
Evaluate side-chains
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 93 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0670
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.3518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.127778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103018 restraints weight = 16052.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.76
r_work: 0.3150 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10612  Z= 0.097
  Angle     :  0.497  10.403  14386  Z= 0.251
  Chirality :  0.039   0.171   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.361 131.431   1522
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.10 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.44 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.24), residues: 1229
  helix:  1.64 (0.20), residues: 660
  sheet: -0.74 (0.51), residues: 99
  loop : -1.34 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 946 
 HIS   0.003   0.000   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.011   0.001   TYR A 927 
 ARG   0.004   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  498)
  hydrogen bonds       : angle       3.99326 ( 1443)
  covalent geometry    : bond        0.00207 (10612)
  covalent geometry    : angle       0.49718 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7903 (tpt-90) cc_final: 0.7683 (tpt-90)
REVERT: A  859 ARG cc_start: 0.6749 (ptt90) cc_final: 0.6511 (ptt-90)
REVERT: A 1094 PHE cc_start: 0.7835 (p90) cc_final: 0.7629 (p90)
REVERT: A 1120 TYR cc_start: 0.7917 (t80) cc_final: 0.7652 (t80)
REVERT: A 1173 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5680 (pp)
REVERT: A 1275 MET cc_start: 0.7984 (mmm) cc_final: 0.7660 (mmt)
REVERT: A 1508 ILE cc_start: 0.8280 (mt) cc_final: 0.7996 (mm)
  outliers start: 6
  outliers final: 5
  residues processed: 124
  average time/residue: 0.3122
  time to fit residues: 52.9668
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0980
   chunk 99 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0870
   chunk 38 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.126732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.102129 restraints weight = 16316.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.78
r_work: 0.3117 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10612  Z= 0.130
  Angle     :  0.531   9.262  14386  Z= 0.272
  Chirality :  0.040   0.173   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.381 129.589   1522
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.83 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.62 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.24), residues: 1229
  helix:  1.54 (0.20), residues: 667
  sheet: -0.80 (0.52), residues: 94
  loop : -1.32 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 474 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.020   0.002   PHE A1186 
 TYR   0.027   0.001   TYR A1510 
 ARG   0.004   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  498)
  hydrogen bonds       : angle       4.11874 ( 1443)
  covalent geometry    : bond        0.00299 (10612)
  covalent geometry    : angle       0.53137 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7773 (tpt-90)
REVERT: A  927 TYR cc_start: 0.6328 (t80) cc_final: 0.6015 (t80)
REVERT: A 1094 PHE cc_start: 0.7925 (p90) cc_final: 0.7688 (p90)
REVERT: A 1120 TYR cc_start: 0.7899 (t80) cc_final: 0.7622 (t80)
REVERT: A 1173 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5641 (pp)
REVERT: A 1399 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5431 (ttt)
REVERT: A 1508 ILE cc_start: 0.8263 (mt) cc_final: 0.7954 (mm)
REVERT: A 1572 VAL cc_start: 0.8250 (t) cc_final: 0.7907 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 122
  average time/residue: 0.3971
  time to fit residues: 67.0779
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1399 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0370
   chunk 117 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 116 optimal weight:    0.0570
   chunk 35 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
A 935 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.100272 restraints weight = 16284.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.91
r_work: 0.3086 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2964 r_free = 0.2964    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10612  Z= 0.102
  Angle     :  0.509   9.292  14386  Z= 0.258
  Chirality :  0.039   0.164   1611
  Planarity :  0.004   0.059   1772
  Dihedral  :  8.346 129.380   1522
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.02 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  9.71 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1229
  helix:  1.62 (0.20), residues: 669
  sheet: -0.73 (0.52), residues: 94
  loop : -1.25 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.024   0.001   TYR A1510 
 ARG   0.004   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  498)
  hydrogen bonds       : angle       4.02720 ( 1443)
  covalent geometry    : bond        0.00220 (10612)
  covalent geometry    : angle       0.50851 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8002 (tpt-90) cc_final: 0.7795 (tpt-90)
REVERT: A  859 ARG cc_start: 0.6750 (ptt90) cc_final: 0.6550 (ptt-90)
REVERT: A  861 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7625 (tp40)
REVERT: A  893 ARG cc_start: 0.6679 (ttt-90) cc_final: 0.5940 (ttp-170)
REVERT: A  927 TYR cc_start: 0.6164 (t80) cc_final: 0.5830 (t80)
REVERT: A 1094 PHE cc_start: 0.7949 (p90) cc_final: 0.7695 (p90)
REVERT: A 1120 TYR cc_start: 0.7883 (t80) cc_final: 0.7545 (t80)
REVERT: A 1173 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5575 (pp)
REVERT: A 1275 MET cc_start: 0.7883 (mmm) cc_final: 0.7573 (mmt)
REVERT: A 1399 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5424 (ttt)
REVERT: A 1508 ILE cc_start: 0.8154 (mt) cc_final: 0.7888 (mm)
  outliers start: 7
  outliers final: 5
  residues processed: 123
  average time/residue: 0.3140
  time to fit residues: 53.8439
Evaluate side-chains
  121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1399 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 112 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 66 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   chunk 118 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 95 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   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 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1404 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.125336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099890 restraints weight = 16085.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.91
r_work: 0.3078 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10612  Z= 0.108
  Angle     :  0.511   9.065  14386  Z= 0.260
  Chirality :  0.039   0.163   1611
  Planarity :  0.004   0.059   1772
  Dihedral  :  8.332 128.656   1522
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 10.07 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1229
  helix:  1.63 (0.20), residues: 669
  sheet: -0.76 (0.52), residues: 94
  loop : -1.24 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.025   0.001   TYR A1510 
 ARG   0.004   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  498)
  hydrogen bonds       : angle       4.04745 ( 1443)
  covalent geometry    : bond        0.00239 (10612)
  covalent geometry    : angle       0.51137 (14386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6684.91 seconds
wall clock time: 121 minutes 52.59 seconds (7312.59 seconds total)