Starting phenix.real_space_refine
on Fri Feb  6 00:14:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hm4_52285/02_2026/9hm4_52285.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     P     157      5.49       5
     Mg      2      5.21       5
     S      20      5.16       5
     C    6493      2.51       5
     N    1929      2.21       5
     O    2581      1.98       5
     H    9612      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20794
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 15760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 958, 15760
          Classifications: {'peptide': 958}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 938}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 1504
          Classifications: {'RNA': 47}
          Modifications used: {'3*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 22, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 3, 'rna3p': 43}
    Chain: "C"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 1085
          Classifications: {'RNA': 34}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 17}
          Link IDs: {'rna2p': 4, 'rna3p': 29}
    Chain: "D"
      Number of atoms: 2443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 2443
          Classifications: {'RNA': 76}
          Modifications used: {'3*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 30, 'rna3p_pyr': 28}
          Link IDs: {'rna2p': 18, 'rna3p': 57}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.02, per 1000 atoms: 0.15
  Number of scatterers: 20794
  At special positions: 0
  Unit cell: (99.19, 134.68, 129.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      20     16.00
     P     157     15.00
     Mg      2     11.99
     O    2581      8.00
     N    1929      7.00
     C    6493      6.00
     H    9612      1.00
    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: 1.80
  Conformation dependent library (CDL) restraints added in 383.5 milliseconds
  

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1832

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      52.3% alpha, 14.1% beta
      55 base pairs and 68 stacking pairs defined.
    Time for finding SS restraints: 3.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.944A  pdb=" N   SER A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LYS A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 292 through 314
      removed outlier: 3.533A  pdb=" N   GLY A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 322
      removed outlier: 3.855A  pdb=" N   ALA A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 349
      removed outlier: 3.641A  pdb=" N   LYS A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 4.689A  pdb=" N   ILE A 353 " --> pdb=" O   ALA A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 370
      removed outlier: 4.206A  pdb=" N   LYS A 363 " --> pdb=" O   ASP A 359 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER A 367 " --> pdb=" O   LYS A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 384
      removed outlier: 3.673A  pdb=" N   GLY A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   MET A 380 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE A 384 " --> pdb=" O   MET A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 418
      removed outlier: 3.858A  pdb=" N   ARG A 395 " --> pdb=" O   SER A 391 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 404 " --> pdb=" O   GLU A 400 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU A 408 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ARG A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   THR A 416 " --> pdb=" O   GLU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 441 through 452
      removed outlier: 4.348A  pdb=" N   ALA A 445 " --> pdb=" O   ARG A 441 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   SER A 446 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN A 449 " --> pdb=" O   ALA A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 480
    Processing helix  chain 'A' and resid 488 through 493
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 516 through 530
      removed outlier: 4.164A  pdb=" N   LYS A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 537
      removed outlier: 3.620A  pdb=" N   GLN A 534 " --> pdb=" O   SER A 530 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 536 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 548
    Processing helix  chain 'A' and resid 555 through 568
      removed outlier: 3.719A  pdb=" N   PHE A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TYR A 568 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 585
      removed outlier: 3.532A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 617
      removed outlier: 4.147A  pdb=" N   TRP A 613 " --> pdb=" O   HIS A 609 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LYS A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   TRP A 617 " --> pdb=" O   TRP A 613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 623
      removed outlier: 3.503A  pdb=" N   LYS A 622 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 647
    Processing helix  chain 'A' and resid 688 through 697
    Processing helix  chain 'A' and resid 725 through 729
    Processing helix  chain 'A' and resid 732 through 742
      removed outlier: 3.759A  pdb=" N   LYS A 742 " --> pdb=" O   ALA A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.604A  pdb=" N   TYR A 746 " --> pdb=" O   LYS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 779
      removed outlier: 3.790A  pdb=" N   LYS A 779 " --> pdb=" O   SER A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 788
    Processing helix  chain 'A' and resid 790 through 801
    Processing helix  chain 'A' and resid 828 through 846
      removed outlier: 4.040A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ALA A 839 " --> pdb=" O   TRP A 835 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE A 844 " --> pdb=" O   GLN A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 866 through 877
    Processing helix  chain 'A' and resid 879 through 885
      removed outlier: 3.511A  pdb=" N   LYS A 885 " --> pdb=" O   LYS A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 900
      removed outlier: 3.795A  pdb=" N   LYS A 893 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 905
    Processing helix  chain 'A' and resid 908 through 916
      removed outlier: 3.805A  pdb=" N   LYS A 914 " --> pdb=" O   VAL A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 966
    Processing helix  chain 'A' and resid 968 through 971
    Processing helix  chain 'A' and resid 972 through 977
    Processing helix  chain 'A' and resid 992 through 995
      removed outlier: 3.685A  pdb=" N   LEU A 995 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 992 through 995'
    Processing helix  chain 'A' and resid 996 through 1024
      removed outlier: 3.738A  pdb=" N   ALA A1003 " --> pdb=" O   ASN A 999 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU A1004 " --> pdb=" O   THR A1000 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY A1010 " --> pdb=" O   ALA A1006 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL A1011 " --> pdb=" O   ASN A1007 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A1022 " --> pdb=" O   HIS A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1046
    Processing helix  chain 'A' and resid 1050 through 1063
      removed outlier: 3.689A  pdb=" N   LEU A1058 " --> pdb=" O   LEU A1054 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLN A1060 " --> pdb=" O   ARG A1056 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LYS A1061 " --> pdb=" O   LYS A1057 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1079
      removed outlier: 4.010A  pdb=" N   VAL A1077 " --> pdb=" O   SER A1073 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA A1079 " --> pdb=" O   MET A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1106
      removed outlier: 3.875A  pdb=" N   GLN A1105 " --> pdb=" O   GLY A1102 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A1106 " --> pdb=" O   THR A1103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1102 through 1106'
    Processing helix  chain 'A' and resid 1135 through 1137
      No H-bonds generated for 'chain 'A' and resid 1135 through 1137'
    Processing helix  chain 'A' and resid 1138 through 1158
      removed outlier: 4.162A  pdb=" N   ASP A1158 " --> pdb=" O   LYS A1154 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463
      removed outlier: 3.918A  pdb=" N   TYR A 423 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA A 425 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   TYR A 638 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA A 212 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLU A 633 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   THR A 669 " --> pdb=" O   GLU A 633 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 463
      removed outlier: 5.204A  pdb=" N   HIS A 434 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ILE A 593 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ILE A 590 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   TYR A 664 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 277
      removed outlier: 6.450A  pdb=" N   THR A 275 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 468
      removed outlier: 3.566A  pdb=" N   GLU A 468 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 810 through 811
      removed outlier: 3.599A  pdb=" N   GLY A 710 " --> pdb=" O   GLY A 722 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ILE A1030 " --> pdb=" O   PHE A 709 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLU A1032 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ASN A 713 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   GLY A1096 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ILE A1029 " --> pdb=" O   GLY A1096 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   ILE A1098 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LYS A1031 " --> pdb=" O   ILE A1098 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 807
      removed outlier: 4.481A  pdb=" N   ILE A 822 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 759 through 761
    Processing sheet with id=AA8, first strand: chain 'A' and resid 857 through 861
      removed outlier: 6.702A  pdb=" N   LEU A 934 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASP A 952 " --> pdb=" O   CYS A 938 " (cutoff:3.500A)

    344 hydrogen bonds defined for protein.
    939 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      140 hydrogen bonds
      256 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      68 stacking parallelities
  Total time for adding SS restraints: 4.48

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9602
        1.03 -     1.23: 48
        1.23 -     1.42: 5275
        1.42 -     1.62: 6364
        1.62 -     1.81: 30
  Bond restraints: 21319
  Sorted by residual:
  bond pdb=" CB  PRO A 210 "
       pdb=" CG  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.492  1.604 -0.112 5.00e-02 4.00e+02 5.06e+00
  bond pdb=" N   PRO A 210 "
       pdb=" CD  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.473  1.497 -0.024 1.40e-02 5.10e+03 2.95e+00
  bond pdb=" N   PRO A 210 "
       pdb=" CA  PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.479  1.451  0.028 1.71e-02 3.42e+03 2.75e+00
  bond pdb=" N   ILE A 578 "
       pdb=" CA  ILE A 578 "
    ideal  model  delta    sigma   weight residual
    1.474  1.460  0.014 1.57e-02 4.06e+03 8.51e-01
  bond pdb=" C   LEU A 209 "
       pdb=" N   PRO A 210 "
    ideal  model  delta    sigma   weight residual
    1.334  1.354 -0.020 2.34e-02 1.83e+03 7.57e-01
  ... (remaining 21314 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.07: 38392
        3.07 -     6.15: 72
        6.15 -     9.22: 3
        9.22 -    12.29: 1
       12.29 -    15.37: 1
  Bond angle restraints: 38469
  Sorted by residual:
  angle pdb=" CA  PRO A 210 "
        pdb=" N   PRO A 210 "
        pdb=" CD  PRO A 210 "
      ideal   model   delta    sigma   weight residual
     112.00   96.63   15.37 1.40e+00 5.10e-01 1.20e+02
  angle pdb=" N   PRO A 210 "
        pdb=" CD  PRO A 210 "
        pdb=" CG  PRO A 210 "
      ideal   model   delta    sigma   weight residual
     103.20   96.57    6.63 1.50e+00 4.44e-01 1.95e+01
  angle pdb=" N   ILE A1111 "
        pdb=" CA  ILE A1111 "
        pdb=" C   ILE A1111 "
      ideal   model   delta    sigma   weight residual
     113.47  109.31    4.16 1.01e+00 9.80e-01 1.69e+01
  angle pdb=" N   VAL A 947 "
        pdb=" CA  VAL A 947 "
        pdb=" C   VAL A 947 "
      ideal   model   delta    sigma   weight residual
     113.71  110.18    3.53 9.50e-01 1.11e+00 1.38e+01
  angle pdb=" N   VAL A 351 "
        pdb=" CA  VAL A 351 "
        pdb=" C   VAL A 351 "
      ideal   model   delta    sigma   weight residual
     111.91  109.03    2.88 8.90e-01 1.26e+00 1.05e+01
  ... (remaining 38464 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.70: 9586
       35.70 -    71.41: 548
       71.41 -   107.11: 64
      107.11 -   142.81: 2
      142.81 -   178.52: 5
  Dihedral angle restraints: 10205
    sinusoidal: 6862
      harmonic: 3343
  Sorted by residual:
  dihedral pdb=" O4'   C D  74 "
           pdb=" C1'   C D  74 "
           pdb=" N1    C D  74 "
           pdb=" C2    C D  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   37.07  162.93     1      1.50e+01 4.44e-03 8.35e+01
  dihedral pdb=" O4'   C D  75 "
           pdb=" C1'   C D  75 "
           pdb=" N1    C D  75 "
           pdb=" C2    C D  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   50.52 -178.52     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C D  72 "
           pdb=" C1'   C D  72 "
           pdb=" N1    C D  72 "
           pdb=" C2    C D  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   39.08 -167.08     1      1.70e+01 3.46e-03 6.56e+01
  ... (remaining 10202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1614
       0.040 -    0.080: 261
       0.080 -    0.119: 69
       0.119 -    0.159: 9
       0.159 -    0.199: 3
  Chirality restraints: 1956
  Sorted by residual:
  chirality pdb=" C1'   C D   5 "
            pdb=" O4'   C D   5 "
            pdb=" C2'   C D   5 "
            pdb=" N1    C D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.27    0.20 2.00e-01 2.50e+01 9.89e-01
  chirality pdb=" CA  PRO A 210 "
            pdb=" N   PRO A 210 "
            pdb=" C   PRO A 210 "
            pdb=" CB  PRO A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" P     G D   1 "
            pdb=" OP1   G D   1 "
            pdb=" OP2   G D   1 "
            pdb=" O5'   G D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.60   -0.19 2.00e-01 2.50e+01 9.28e-01
  ... (remaining 1953 not shown)

  Planarity restraints: 2586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 209 "    0.085 5.00e-02 4.00e+02   1.18e-01 2.24e+01
        pdb=" N   PRO A 210 "   -0.204 5.00e-02 4.00e+02
        pdb=" CA  PRO A 210 "    0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO A 210 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C D   5 "   -0.029 2.00e-02 2.50e+03   1.38e-02 5.21e+00
        pdb=" N1    C D   5 "    0.033 2.00e-02 2.50e+03
        pdb=" C2    C D   5 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    C D   5 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    C D   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C D   5 "   -0.006 2.00e-02 2.50e+03
        pdb=" N4    C D   5 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    C D   5 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    C D   5 "    0.003 2.00e-02 2.50e+03
        pdb=" H5    C D   5 "   -0.003 2.00e-02 2.50e+03
        pdb=" H6    C D   5 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G D  19 "    0.023 2.00e-02 2.50e+03   8.80e-03 2.71e+00
        pdb=" N9    G D  19 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    G D  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G D  19 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G D  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G D  19 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G D  19 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    G D  19 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G D  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G D  19 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G D  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G D  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" H8    G D  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" H1    G D  19 "    0.003 2.00e-02 2.50e+03
  ... (remaining 2583 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 927
        2.18 -     2.78: 37786
        2.78 -     3.39: 52728
        3.39 -     3.99: 69576
        3.99 -     4.60: 107687
  Nonbonded interactions: 268704
  Sorted by model distance:
  nonbonded pdb="HH22 ARG A 473 "
            pdb=" OP1   C C  35 "
     model   vdw
     1.574 2.450
  nonbonded pdb="HO2'   G D  35 "
            pdb=" O4'   C D  36 "
     model   vdw
     1.575 2.450
  nonbonded pdb=" O   PRO A 774 "
            pdb=" H   PHE A 777 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" HZ2 LYS A 766 "
            pdb=" OP2   G B  28 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OE1 GLU A 715 "
            pdb="HO2'   C D  74 "
     model   vdw
     1.608 2.450
  ... (remaining 268699 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.040
  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:             0.080
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.060
  Find NCS groups from input model:        0.050
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.112  11707  Z= 0.130
  Angle     :  0.595  15.367  16517  Z= 0.350
  Chirality :  0.035   0.199   1956
  Planarity :  0.004   0.118   1531
  Dihedral  : 20.253 178.517   5508
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.32 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  9.94 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.27), residues: 950
  helix: -1.38 (0.25), residues: 404
  sheet: -1.62 (0.45), residues: 112
  loop : -0.99 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 917 
 TYR   0.017   0.001   TYR A 979 
 PHE   0.008   0.001   PHE A 725 
 TRP   0.014   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A1117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11707)
  covalent geometry    : angle       0.59515 (16517)
  hydrogen bonds       : bond        0.23903 (  480)
  hydrogen bonds       : angle       8.20404 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 68
  average time/residue: 0.3046
  time to fit residues: 27.2555
Evaluate side-chains
  67 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  763 TYR
Chi-restraints excluded: chain A residue 1115 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 795 GLN
A 974 GLN
A 999 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.175946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.129423 restraints weight = 45032.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 2.63
r_work: 0.3796 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11707  Z= 0.203
  Angle     :  0.607   5.461  16517  Z= 0.333
  Chirality :  0.037   0.173   1956
  Planarity :  0.004   0.046   1531
  Dihedral  : 21.163 177.773   3483
  Min Nonbonded Distance : 1.819

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 10.06 %
    Favored  : 88.79 %
  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: -1.62 (0.26), residues: 950
  helix: -0.72 (0.25), residues: 425
  sheet: -1.29 (0.45), residues: 110
  loop : -1.23 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 917 
 TYR   0.018   0.002   TYR A 979 
 PHE   0.015   0.002   PHE A1034 
 TRP   0.008   0.001   TRP A 424 
 HIS   0.004   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (11707)
  covalent geometry    : angle       0.60744 (16517)
  hydrogen bonds       : bond        0.06600 (  480)
  hydrogen bonds       : angle       5.28409 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  715 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7012 (mt-10)
REVERT: A  888 ASP cc_start: 0.8215 (m-30) cc_final: 0.7891 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.3105
  time to fit residues: 30.8035
Evaluate side-chains
  74 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  658 ARG
Chi-restraints excluded: chain A residue  763 TYR
Chi-restraints excluded: chain A residue  974 GLN
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0670
   chunk 69 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.8920

-------------------------------------------------------------------------------
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 = 0.4542 r_free = 0.4542 target = 0.177998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.134691 restraints weight = 44896.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 2.65
r_work: 0.3822 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7116
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11707  Z= 0.128
  Angle     :  0.536   5.732  16517  Z= 0.292
  Chirality :  0.035   0.170   1956
  Planarity :  0.003   0.038   1531
  Dihedral  : 21.057 176.015   3483
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.95 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.33 %
    Favored  : 87.28 %
  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: -1.26 (0.27), residues: 950
  helix: -0.29 (0.25), residues: 430
  sheet: -1.07 (0.46), residues: 111
  loop : -1.25 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 841 
 TYR   0.017   0.001   TYR A 979 
 PHE   0.010   0.001   PHE A1034 
 TRP   0.007   0.001   TRP A 466 
 HIS   0.002   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (11707)
  covalent geometry    : angle       0.53553 (16517)
  hydrogen bonds       : bond        0.05368 (  480)
  hydrogen bonds       : angle       4.69359 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8292 (p90) cc_final: 0.7883 (p90)
REVERT: A  547 ASP cc_start: 0.8660 (t70) cc_final: 0.8369 (t0)
REVERT: A  601 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  715 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6984 (mt-10)
REVERT: A  888 ASP cc_start: 0.7894 (m-30) cc_final: 0.7389 (t0)
REVERT: A 1019 TYR cc_start: 0.7664 (m-80) cc_final: 0.7381 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 79
  average time/residue: 0.2756
  time to fit residues: 29.3565
Evaluate side-chains
  73 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 106 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
A 974 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.175682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.131758 restraints weight = 45411.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 2.71
r_work: 0.3778 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11707  Z= 0.150
  Angle     :  0.534   6.181  16517  Z= 0.290
  Chirality :  0.035   0.168   1956
  Planarity :  0.003   0.040   1531
  Dihedral  : 21.000 174.942   3481
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.56 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.27), residues: 950
  helix: -0.06 (0.26), residues: 431
  sheet: -0.73 (0.49), residues: 97
  loop : -1.34 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 917 
 TYR   0.016   0.001   TYR A 979 
 PHE   0.013   0.001   PHE A1034 
 TRP   0.009   0.001   TRP A 897 
 HIS   0.003   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (11707)
  covalent geometry    : angle       0.53371 (16517)
  hydrogen bonds       : bond        0.05076 (  480)
  hydrogen bonds       : angle       4.44371 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8338 (p90) cc_final: 0.7921 (p90)
REVERT: A  547 ASP cc_start: 0.8667 (t70) cc_final: 0.8334 (t0)
REVERT: A  715 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7045 (mt-10)
REVERT: A  888 ASP cc_start: 0.7849 (m-30) cc_final: 0.7337 (t0)
REVERT: A  945 GLN cc_start: 0.8741 (mt0) cc_final: 0.8540 (mt0)
REVERT: A  960 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.5868 (ttt-90)
  outliers start: 15
  outliers final: 12
  residues processed: 86
  average time/residue: 0.2820
  time to fit residues: 32.3843
Evaluate side-chains
  80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  283 MET
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  686 ASP
Chi-restraints excluded: chain A residue  866 THR
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 100 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 72 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 105 optimal weight:   30.0000
   chunk 54 optimal weight:    2.9990
   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 = 0.4539 r_free = 0.4539 target = 0.177855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.132780 restraints weight = 45041.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 2.82
r_work: 0.3817 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11707  Z= 0.107
  Angle     :  0.496   6.548  16517  Z= 0.268
  Chirality :  0.034   0.153   1956
  Planarity :  0.003   0.035   1531
  Dihedral  : 20.898 173.948   3481
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.63 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.72 %
    Favored  : 86.24 %
  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: -0.77 (0.27), residues: 950
  helix:  0.24 (0.26), residues: 431
  sheet: -0.74 (0.49), residues: 92
  loop : -1.18 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 334 
 TYR   0.013   0.001   TYR A 979 
 PHE   0.009   0.001   PHE A1034 
 TRP   0.007   0.001   TRP A 424 
 HIS   0.002   0.001   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (11707)
  covalent geometry    : angle       0.49568 (16517)
  hydrogen bonds       : bond        0.04349 (  480)
  hydrogen bonds       : angle       4.16096 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8318 (p90) cc_final: 0.7869 (p90)
REVERT: A  547 ASP cc_start: 0.8674 (t70) cc_final: 0.8322 (t0)
REVERT: A  601 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7595 (pp20)
REVERT: A  715 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7008 (mt-10)
  outliers start: 9
  outliers final: 9
  residues processed: 78
  average time/residue: 0.2820
  time to fit residues: 29.6656
Evaluate side-chains
  72 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 104 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.5986

-------------------------------------------------------------------------------
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 = 0.4502 r_free = 0.4502 target = 0.174744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.130383 restraints weight = 45169.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 2.72
r_work: 0.3765 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11707  Z= 0.189
  Angle     :  0.549   7.460  16517  Z= 0.297
  Chirality :  0.036   0.177   1956
  Planarity :  0.004   0.065   1531
  Dihedral  : 20.942 173.840   3481
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.47 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.49 %
    Favored  : 85.32 %
  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: -0.93 (0.27), residues: 950
  helix:  0.11 (0.26), residues: 432
  sheet: -0.79 (0.49), residues: 92
  loop : -1.27 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1114 
 TYR   0.017   0.001   TYR A 979 
 PHE   0.014   0.002   PHE A1034 
 TRP   0.010   0.001   TRP A 897 
 HIS   0.004   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (11707)
  covalent geometry    : angle       0.54940 (16517)
  hydrogen bonds       : bond        0.05243 (  480)
  hydrogen bonds       : angle       4.35209 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8362 (p90) cc_final: 0.7918 (p90)
REVERT: A  547 ASP cc_start: 0.8663 (t70) cc_final: 0.8301 (t0)
REVERT: A  601 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7669 (pp20)
REVERT: A  715 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7114 (mt-10)
REVERT: A  960 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5850 (ttt-90)
  outliers start: 19
  outliers final: 17
  residues processed: 84
  average time/residue: 0.2735
  time to fit residues: 30.6648
Evaluate side-chains
  82 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  686 ASP
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1078 ARG
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1110 CYS
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1157 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.174630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.130753 restraints weight = 45435.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.75
r_work: 0.3763 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11707  Z= 0.179
  Angle     :  0.546   6.910  16517  Z= 0.295
  Chirality :  0.036   0.179   1956
  Planarity :  0.003   0.041   1531
  Dihedral  : 20.923 173.204   3481
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.58 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.37 %
    Favored  : 85.43 %
  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: -0.98 (0.27), residues: 950
  helix:  0.11 (0.26), residues: 432
  sheet: -0.86 (0.49), residues: 92
  loop : -1.33 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1114 
 TYR   0.014   0.001   TYR A 979 
 PHE   0.013   0.001   PHE A1034 
 TRP   0.009   0.001   TRP A 897 
 HIS   0.003   0.001   HIS A1134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11707)
  covalent geometry    : angle       0.54576 (16517)
  hydrogen bonds       : bond        0.05167 (  480)
  hydrogen bonds       : angle       4.35279 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8364 (p90) cc_final: 0.7914 (p90)
REVERT: A  547 ASP cc_start: 0.8703 (t70) cc_final: 0.8391 (t0)
REVERT: A  601 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7743 (pp20)
REVERT: A  715 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7170 (mt-10)
REVERT: A  960 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5991 (ttt-90)
  outliers start: 19
  outliers final: 18
  residues processed: 84
  average time/residue: 0.2608
  time to fit residues: 29.3583
Evaluate side-chains
  83 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  670 ILE
Chi-restraints excluded: chain A residue  686 ASP
Chi-restraints excluded: chain A residue  866 THR
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1078 ARG
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1110 CYS
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1157 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 69 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.177224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.133829 restraints weight = 45067.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.74
r_work: 0.3802 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11707  Z= 0.108
  Angle     :  0.500   7.184  16517  Z= 0.270
  Chirality :  0.034   0.154   1956
  Planarity :  0.003   0.039   1531
  Dihedral  : 20.853 172.190   3481
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.84 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.83 %
    Favored  : 85.32 %
  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: -0.61 (0.28), residues: 950
  helix:  0.41 (0.26), residues: 432
  sheet: -0.57 (0.49), residues: 93
  loop : -1.17 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.011   0.001   TYR A 979 
 PHE   0.009   0.001   PHE A1034 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (11707)
  covalent geometry    : angle       0.49951 (16517)
  hydrogen bonds       : bond        0.04395 (  480)
  hydrogen bonds       : angle       4.08681 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8314 (p90) cc_final: 0.7883 (p90)
REVERT: A  547 ASP cc_start: 0.8692 (t70) cc_final: 0.8363 (t0)
REVERT: A  601 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7768 (pp20)
REVERT: A  715 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7130 (mt-10)
REVERT: A  960 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5883 (ttt-90)
REVERT: A  979 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7382 (p90)
  outliers start: 16
  outliers final: 12
  residues processed: 84
  average time/residue: 0.2545
  time to fit residues: 28.9719
Evaluate side-chains
  81 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  979 TYR
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1078 ARG
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1110 CYS
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 100 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.177931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.133635 restraints weight = 44840.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.74
r_work: 0.3825 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  11707  Z= 0.102
  Angle     :  0.484   7.440  16517  Z= 0.261
  Chirality :  0.033   0.153   1956
  Planarity :  0.003   0.038   1531
  Dihedral  : 20.765 170.283   3481
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.63 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.06 %
    Favored  : 85.32 %
  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: -0.42 (0.28), residues: 950
  helix:  0.61 (0.27), residues: 432
  sheet: -0.41 (0.50), residues: 93
  loop : -1.14 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.010   0.001   TYR A 979 
 PHE   0.014   0.001   PHE A 511 
 TRP   0.006   0.001   TRP A 897 
 HIS   0.002   0.001   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (11707)
  covalent geometry    : angle       0.48370 (16517)
  hydrogen bonds       : bond        0.04141 (  480)
  hydrogen bonds       : angle       3.94512 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8310 (p90) cc_final: 0.7834 (p90)
REVERT: A  364 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7172 (mt-10)
REVERT: A  547 ASP cc_start: 0.8701 (t70) cc_final: 0.8371 (t0)
REVERT: A  601 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7832 (pp20)
REVERT: A  715 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7080 (mt-10)
REVERT: A  882 GLU cc_start: 0.8509 (tp30) cc_final: 0.8258 (tp30)
REVERT: A  960 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5827 (ttt-90)
REVERT: A  979 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7252 (p90)
  outliers start: 14
  outliers final: 11
  residues processed: 80
  average time/residue: 0.2494
  time to fit residues: 26.9783
Evaluate side-chains
  80 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  979 TYR
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1078 ARG
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1110 CYS
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 73 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.177833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.133485 restraints weight = 44906.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 2.74
r_work: 0.3820 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  11707  Z= 0.110
  Angle     :  0.486   7.423  16517  Z= 0.262
  Chirality :  0.033   0.152   1956
  Planarity :  0.003   0.037   1531
  Dihedral  : 20.739 170.158   3481
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.84 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.29 %
    Favored  : 85.09 %
  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: -0.33 (0.28), residues: 950
  helix:  0.71 (0.27), residues: 432
  sheet: -0.31 (0.50), residues: 93
  loop : -1.14 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.010   0.001   TYR A 979 
 PHE   0.010   0.001   PHE A1034 
 TRP   0.007   0.001   TRP A 897 
 HIS   0.002   0.001   HIS A1018 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (11707)
  covalent geometry    : angle       0.48568 (16517)
  hydrogen bonds       : bond        0.04043 (  480)
  hydrogen bonds       : angle       3.91961 ( 1195)

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

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

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1900 Ramachandran restraints generated.
    950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TYR cc_start: 0.8312 (p90) cc_final: 0.7839 (p90)
REVERT: A  364 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7148 (mt-10)
REVERT: A  520 LYS cc_start: 0.7283 (mttp) cc_final: 0.7073 (mttp)
REVERT: A  547 ASP cc_start: 0.8712 (t70) cc_final: 0.8384 (t0)
REVERT: A  601 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7887 (pp20)
REVERT: A  715 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7141 (mt-10)
REVERT: A  960 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5832 (ttt-90)
REVERT: A  979 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7391 (p90)
  outliers start: 14
  outliers final: 12
  residues processed: 84
  average time/residue: 0.2893
  time to fit residues: 33.0569
Evaluate side-chains
  83 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  490 PHE
Chi-restraints excluded: chain A residue  661 HIS
Chi-restraints excluded: chain A residue  938 CYS
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue  976 ILE
Chi-restraints excluded: chain A residue  979 TYR
Chi-restraints excluded: chain A residue 1034 PHE
Chi-restraints excluded: chain A residue 1064 ASN
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1078 ARG
Chi-restraints excluded: chain A residue 1083 GLU
Chi-restraints excluded: chain A residue 1110 CYS
Chi-restraints excluded: chain A residue 1115 LEU
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.177700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.134690 restraints weight = 44880.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.70
r_work: 0.3814 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11707  Z= 0.113
  Angle     :  0.487   7.476  16517  Z= 0.262
  Chirality :  0.033   0.152   1956
  Planarity :  0.003   0.037   1531
  Dihedral  : 20.733 169.705   3481
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  5.05 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.53 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.28), residues: 950
  helix:  0.79 (0.27), residues: 433
  sheet: -0.31 (0.50), residues: 93
  loop : -1.16 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 473 
 TYR   0.010   0.001   TYR A 979 
 PHE   0.014   0.001   PHE A 511 
 TRP   0.007   0.001   TRP A 897 
 HIS   0.002   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (11707)
  covalent geometry    : angle       0.48741 (16517)
  hydrogen bonds       : bond        0.04057 (  480)
  hydrogen bonds       : angle       3.91779 ( 1195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4914.95 seconds
wall clock time: 84 minutes 5.74 seconds (5045.74 seconds total)