Starting phenix.real_space_refine
on Fri Sep 11 05:08:51 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e7s_31003/09_2026/7e7s_31003.cif"
  }
  resolution = 3.3
  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=   0.007
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
     Ca      2      9.91       5
     S      58      5.16       5
     C    5027      2.51       5
     N    1314      2.21       5
     O    1483      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7884
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1020, 7882
          Classifications: {'peptide': 1020}
          Link IDs: {'PTRANS': 46, 'TRANS': 973}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.74, per 1000 atoms: 0.22
  Number of scatterers: 7884
  At special positions: 0
  Unit cell: (78.435, 84.66, 150.645, 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)
     Ca      2     19.99
     S      58     16.00
     O    1483      8.00
     N    1314      7.00
     C    5027      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 875 " - pdb=" SG  CYS A 887 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 412.0 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      55.0% alpha, 14.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 7
      removed outlier: 3.599A  pdb=" N   THR A   6 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LYS A   7 " --> pdb=" O   ALA A   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 3 through 7'
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.588A  pdb=" N   GLU A  34 " --> pdb=" O   LYS A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 76
    Processing helix  chain 'A' and resid 88 through 123
      removed outlier: 3.509A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A  94 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.976A  pdb=" N   ASN A 229 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 3.748A  pdb=" N   HIS A 278 " --> pdb=" O   ASN A 275 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.631A  pdb=" N   PHE A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 329
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.690A  pdb=" N   THR A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 345
      No H-bonds generated for 'chain 'A' and resid 343 through 345'
    Processing helix  chain 'A' and resid 407 through 420
      removed outlier: 3.745A  pdb=" N   VAL A 411 " --> pdb=" O   TYR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 463 through 468
      removed outlier: 4.106A  pdb=" N   ALA A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 478
    Processing helix  chain 'A' and resid 516 through 523
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.622A  pdb=" N   GLN A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 3.859A  pdb=" N   PHE A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 3.502A  pdb=" N   ASN A 671 " --> pdb=" O   ASP A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.868A  pdb=" N   LYS A 683 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   SER A 684 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 705
      No H-bonds generated for 'chain 'A' and resid 703 through 705'
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 723 through 729
      removed outlier: 3.639A  pdb=" N   LYS A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 781
      removed outlier: 3.705A  pdb=" N   VAL A 743 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 800
      removed outlier: 3.676A  pdb=" N   GLY A 800 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 858
      removed outlier: 3.557A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A 858 " --> pdb=" O   TRP A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 891
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.425A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 916
      No H-bonds generated for 'chain 'A' and resid 914 through 916'
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 946
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.621A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.632A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 153
      removed outlier: 6.861A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ILE A 163 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 208 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176
      removed outlier: 6.552A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASN A 213 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 651 through 653
      removed outlier: 8.069A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.675A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 734 " --> pdb=" O   ALA A 718 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   LEU A 563 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 4.853A  pdb=" N   CYS A 595 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU A 561 " --> pdb=" O   CYS A 595 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLY A 597 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   ARG A 559 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 515 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   ALA A 564 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   THR A 499 " --> pdb=" O   LYS A 481 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   LYS A 481 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396
      removed outlier: 7.446A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 368 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ARG A 365 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.199A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.034A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.946A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   CYS A 524 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 592 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   HIS A 526 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   GLY A 594 " --> pdb=" O   HIS A 526 " (cutoff:3.500A)
      removed outlier: 9.299A  pdb=" N   ARG A 528 " --> pdb=" O   GLY A 594 " (cutoff:3.500A)
      removed outlier: 13.026A  pdb=" N   VAL A 596 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428

    413 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2577
        1.34 -     1.46: 1658
        1.46 -     1.58: 3706
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 8031
  Sorted by residual:
  bond pdb=" CA  VAL A 529 "
       pdb=" CB  VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.72e-01
  bond pdb=" CG  LEU A 806 "
       pdb=" CD1 LEU A 806 "
    ideal  model  delta    sigma   weight residual
    1.521  1.498  0.023 3.30e-02 9.18e+02 4.87e-01
  bond pdb=" N   PRO A 819 "
       pdb=" CA  PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.31e-02 5.83e+03 4.68e-01
  bond pdb=" C   PRO A 819 "
       pdb=" O   PRO A 819 "
    ideal  model  delta    sigma   weight residual
    1.246  1.240  0.005 8.50e-03 1.38e+04 4.18e-01
  bond pdb=" CG  PRO A 312 "
       pdb=" CD  PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.503  1.481  0.022 3.40e-02 8.65e+02 4.14e-01
  ... (remaining 8026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 10771
        1.66 -     3.32: 94
        3.32 -     4.98: 26
        4.98 -     6.64: 7
        6.64 -     8.30: 1
  Bond angle restraints: 10899
  Sorted by residual:
  angle pdb=" CB  MET A 908 "
        pdb=" CG  MET A 908 "
        pdb=" SD  MET A 908 "
      ideal   model   delta    sigma   weight residual
     112.70  121.00   -8.30 3.00e+00 1.11e-01 7.65e+00
  angle pdb=" N   ILE A 232 "
        pdb=" CA  ILE A 232 "
        pdb=" C   ILE A 232 "
      ideal   model   delta    sigma   weight residual
     113.07  109.43    3.64 1.36e+00 5.41e-01 7.18e+00
  angle pdb=" C   VAL A 223 "
        pdb=" N   VAL A 224 "
        pdb=" CA  VAL A 224 "
      ideal   model   delta    sigma   weight residual
     122.66  120.19    2.47 9.70e-01 1.06e+00 6.46e+00
  angle pdb=" CB  LYS A 541 "
        pdb=" CG  LYS A 541 "
        pdb=" CD  LYS A 541 "
      ideal   model   delta    sigma   weight residual
     111.30  116.95   -5.65 2.30e+00 1.89e-01 6.04e+00
  angle pdb=" N   LEU A 952 "
        pdb=" CA  LEU A 952 "
        pdb=" C   LEU A 952 "
      ideal   model   delta    sigma   weight residual
     109.81  115.21   -5.40 2.21e+00 2.05e-01 5.98e+00
  ... (remaining 10894 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 4353
       17.73 -    35.45: 426
       35.45 -    53.18: 64
       53.18 -    70.91: 17
       70.91 -    88.63: 8
  Dihedral angle restraints: 4868
    sinusoidal: 1922
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.07  -22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ASP A1038 "
           pdb=" CB  ASP A1038 "
           pdb=" CG  ASP A1038 "
           pdb=" OD1 ASP A1038 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.97   58.97     1      2.00e+01 2.50e-03 1.16e+01
  dihedral pdb=" CB  GLU A  79 "
           pdb=" CG  GLU A  79 "
           pdb=" CD  GLU A  79 "
           pdb=" OE1 GLU A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.63  -88.63     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 919
       0.036 -    0.072: 256
       0.072 -    0.108: 85
       0.108 -    0.144: 18
       0.144 -    0.180: 1
  Chirality restraints: 1279
  Sorted by residual:
  chirality pdb=" CB  ILE A 150 "
            pdb=" CA  ILE A 150 "
            pdb=" CG1 ILE A 150 "
            pdb=" CG2 ILE A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  PRO A 788 "
            pdb=" N   PRO A 788 "
            pdb=" C   PRO A 788 "
            pdb=" CB  PRO A 788 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.96e-01
  ... (remaining 1276 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 400 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO A 401 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 401 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 401 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 247 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO A 248 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 248 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 248 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 892 "   -0.025 5.00e-02 4.00e+02   3.87e-02 2.39e+00
        pdb=" N   PRO A 893 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 893 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 893 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 222
        2.71 -     3.26: 8253
        3.26 -     3.81: 12642
        3.81 -     4.35: 15906
        4.35 -     4.90: 26753
  Nonbonded interactions: 63776
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 879 "
            pdb=" OD1 ASP A 881 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   ILE A 307 "
            pdb=" OE1 GLU A 309 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NH2 ARG A 619 "
            pdb=" O   CYS A 669 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   PHE A 209 "
            pdb=" OG1 THR A 212 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER A  38 "
            pdb=" O   LYS A 143 "
     model   vdw
     2.296 3.040
  ... (remaining 63771 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.500
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8032  Z= 0.113
  Angle     :  0.496   8.299  10901  Z= 0.261
  Chirality :  0.040   0.180   1279
  Planarity :  0.004   0.054   1389
  Dihedral  : 14.410  88.632   2955
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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: -0.13 (0.26), residues: 1014
  helix:  0.30 (0.23), residues: 482
  sheet: -1.14 (0.48), residues: 109
  loop : -0.03 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.008   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A1040 
 TRP   0.007   0.001   TRP A 272 
 HIS   0.001   0.000   HIS A 396 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.11 ( 8031)
  covalent geometry    : angle       0.49597 /  0.26 (10899)
  SS BOND              : bond        0.00073 /  0.04 (    1)
  SS BOND              : angle       0.60668 /  0.35 (    2)
  hydrogen bonds       : bond        0.24706 / 16.16 (  403)
  hydrogen bonds       : angle       7.94273 /  5.70 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  126 MET cc_start: 0.7479 (mmm) cc_final: 0.7023 (tmm)
REVERT: A  399 ASP cc_start: 0.6887 (t70) cc_final: 0.6640 (t70)
REVERT: A  568 ASN cc_start: 0.7578 (t0) cc_final: 0.7082 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0867
  time to fit residues: 12.8419
Evaluate side-chains
  81 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 275 ASN
A 403 ASN
A 691 GLN
A 913 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.184929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115323 restraints weight = 8357.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.04
r_work: 0.2989 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8032  Z= 0.135
  Angle     :  0.538   7.143  10901  Z= 0.281
  Chirality :  0.042   0.178   1279
  Planarity :  0.004   0.048   1389
  Dihedral  :  3.869  22.242   1078
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  6.30 %
    Favored  : 93.36 %
  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:  0.64 (0.27), residues: 1014
  helix:  1.26 (0.23), residues: 501
  sheet: -1.24 (0.46), residues: 105
  loop : -0.02 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 619 
 TYR   0.017   0.001   TYR A 842 
 PHE   0.009   0.001   PHE A 367 
 TRP   0.006   0.001   TRP A 854 
 HIS   0.003   0.001   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.13 ( 8031)
  covalent geometry    : angle       0.53833 /  0.28 (10899)
  SS BOND              : bond        0.00056 /  0.03 (    1)
  SS BOND              : angle       0.39389 /  0.22 (    2)
  hydrogen bonds       : bond        0.05269 /  3.44 (  403)
  hydrogen bonds       : angle       5.17718 /  3.58 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  467 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7440 (tpp-160)
REVERT: A  482 GLU cc_start: 0.6873 (mp0) cc_final: 0.6145 (mp0)
REVERT: A  568 ASN cc_start: 0.7845 (t0) cc_final: 0.7365 (p0)
REVERT: A  586 TYR cc_start: 0.6633 (m-10) cc_final: 0.6277 (m-10)
REVERT: A  714 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8379 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 104
  average time/residue: 0.0853
  time to fit residues: 12.5188
Evaluate side-chains
  90 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  437 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 52 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.1786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.183756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111630 restraints weight = 8293.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.89
r_work: 0.3006 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8032  Z= 0.142
  Angle     :  0.519   5.933  10901  Z= 0.267
  Chirality :  0.042   0.154   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.879  24.073   1078
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 10.42 %
    Favored  : 89.12 %
  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:  0.80 (0.27), residues: 1014
  helix:  1.47 (0.23), residues: 501
  sheet: -0.89 (0.51), residues: 92
  loop : -0.18 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.017   0.001   TYR A 842 
 PHE   0.013   0.001   PHE A1040 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.14 ( 8031)
  covalent geometry    : angle       0.51862 /  0.27 (10899)
  SS BOND              : bond        0.00121 /  0.06 (    1)
  SS BOND              : angle       0.46180 /  0.27 (    2)
  hydrogen bonds       : bond        0.04515 /  2.96 (  403)
  hydrogen bonds       : angle       4.82779 /  3.32 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  482 GLU cc_start: 0.6723 (mp0) cc_final: 0.6082 (mp0)
REVERT: A  553 SER cc_start: 0.8142 (t) cc_final: 0.7820 (p)
REVERT: A  568 ASN cc_start: 0.7826 (t0) cc_final: 0.7382 (p0)
REVERT: A  585 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7674 (pttp)
REVERT: A  586 TYR cc_start: 0.6569 (m-10) cc_final: 0.6245 (m-80)
REVERT: A  626 ASP cc_start: 0.7900 (t70) cc_final: 0.7658 (t0)
REVERT: A  898 MET cc_start: 0.8994 (mmm) cc_final: 0.8757 (mmm)
  outliers start: 4
  outliers final: 2
  residues processed: 98
  average time/residue: 0.0903
  time to fit residues: 12.2589
Evaluate side-chains
  93 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  663 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 75 optimal weight:    1.9990
   chunk 101 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0050
   chunk 80 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 24 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.3372

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.185797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.113346 restraints weight = 8498.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.06
r_work: 0.3024 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8032  Z= 0.096
  Angle     :  0.485   6.507  10901  Z= 0.247
  Chirality :  0.040   0.132   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.738  22.422   1078
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.68 %
    Favored  : 87.17 %
  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:  1.11 (0.27), residues: 1014
  helix:  1.79 (0.24), residues: 501
  sheet: -0.46 (0.59), residues: 74
  loop : -0.22 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 549 
 TYR   0.013   0.001   TYR A 842 
 PHE   0.010   0.001   PHE A1040 
 TRP   0.007   0.001   TRP A 793 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00207 /  0.10 ( 8031)
  covalent geometry    : angle       0.48514 /  0.25 (10899)
  SS BOND              : bond        0.00085 /  0.04 (    1)
  SS BOND              : angle       0.30879 /  0.17 (    2)
  hydrogen bonds       : bond        0.03638 /  2.39 (  403)
  hydrogen bonds       : angle       4.43945 /  3.05 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A  479 MET cc_start: 0.7073 (tpt) cc_final: 0.6846 (tpt)
REVERT: A  482 GLU cc_start: 0.6590 (mp0) cc_final: 0.6129 (mp0)
REVERT: A  568 ASN cc_start: 0.7682 (t0) cc_final: 0.7307 (p0)
REVERT: A  585 LYS cc_start: 0.7910 (ptpp) cc_final: 0.7631 (pttp)
REVERT: A  586 TYR cc_start: 0.6655 (m-10) cc_final: 0.6417 (m-10)
REVERT: A  763 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8561 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 103
  average time/residue: 0.0863
  time to fit residues: 12.5283
Evaluate side-chains
  98 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 92 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 90 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.6108 > 50:)
   chunk 23 optimal weight:    0.1980
   chunk 1 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   chunk 20 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 879 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.187352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.115855 restraints weight = 8380.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 1.89
r_work: 0.3029 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8032  Z= 0.101
  Angle     :  0.487   6.582  10901  Z= 0.246
  Chirality :  0.041   0.169   1279
  Planarity :  0.004   0.046   1389
  Dihedral  :  3.722  22.987   1078
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.40 %
    Favored  : 85.22 %
  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:  1.17 (0.27), residues: 1014
  helix:  1.87 (0.24), residues: 500
  sheet: -0.27 (0.69), residues: 62
  loop : -0.27 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.015   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A1040 
 TRP   0.007   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.10 ( 8031)
  covalent geometry    : angle       0.48694 /  0.25 (10899)
  SS BOND              : bond        0.00125 /  0.07 (    1)
  SS BOND              : angle       0.39140 /  0.22 (    2)
  hydrogen bonds       : bond        0.03583 /  2.36 (  403)
  hydrogen bonds       : angle       4.33659 /  2.99 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6823 (mtm-85) cc_final: 0.6600 (mtm-85)
REVERT: A  479 MET cc_start: 0.6978 (tpt) cc_final: 0.6730 (tpt)
REVERT: A  482 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6043 (mp0)
REVERT: A  549 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.6735 (mtm110)
REVERT: A  553 SER cc_start: 0.8097 (t) cc_final: 0.7825 (p)
REVERT: A  568 ASN cc_start: 0.7687 (t0) cc_final: 0.7344 (p0)
REVERT: A  585 LYS cc_start: 0.7911 (ptpp) cc_final: 0.7630 (pttp)
REVERT: A  586 TYR cc_start: 0.6732 (m-10) cc_final: 0.6512 (m-10)
REVERT: A  693 PHE cc_start: 0.7776 (m-80) cc_final: 0.7547 (m-80)
REVERT: A  763 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8621 (mp)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0860
  time to fit residues: 12.2062
Evaluate side-chains
  100 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.0970
   chunk 24 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0370
   chunk 92 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.5456

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.187252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.115855 restraints weight = 8339.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.90
r_work: 0.3036 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8032  Z= 0.099
  Angle     :  0.489   7.113  10901  Z= 0.245
  Chirality :  0.041   0.146   1279
  Planarity :  0.003   0.046   1389
  Dihedral  :  3.682  22.767   1078
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.97 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.20 (0.27), residues: 1014
  helix:  1.94 (0.24), residues: 499
  sheet: -0.56 (0.72), residues: 52
  loop : -0.28 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.015   0.001   TYR A 842 
 PHE   0.011   0.001   PHE A1040 
 TRP   0.007   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.10 ( 8031)
  covalent geometry    : angle       0.48912 /  0.24 (10899)
  SS BOND              : bond        0.00125 /  0.07 (    1)
  SS BOND              : angle       0.40831 /  0.24 (    2)
  hydrogen bonds       : bond        0.03444 /  2.27 (  403)
  hydrogen bonds       : angle       4.25261 /  2.92 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6635 (mtm-85)
REVERT: A  479 MET cc_start: 0.6989 (tpt) cc_final: 0.6727 (tpt)
REVERT: A  482 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6095 (mp0)
REVERT: A  549 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6804 (mtm110)
REVERT: A  553 SER cc_start: 0.8029 (t) cc_final: 0.7769 (p)
REVERT: A  568 ASN cc_start: 0.7730 (t0) cc_final: 0.7450 (p0)
REVERT: A  585 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7630 (pttp)
REVERT: A  763 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8624 (mp)
  outliers start: 12
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0845
  time to fit residues: 12.5950
Evaluate side-chains
  101 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  575 MET
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 91 optimal weight:    0.2980
   chunk 17 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0970
   chunk 52 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 691 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108449 restraints weight = 8597.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.07
r_work: 0.3019 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8032  Z= 0.101
  Angle     :  0.493   7.467  10901  Z= 0.248
  Chirality :  0.041   0.231   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.674  22.764   1078
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.43 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.25 (0.27), residues: 1014
  helix:  1.96 (0.24), residues: 500
  sheet: -0.30 (0.68), residues: 62
  loop : -0.27 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.015   0.001   TYR A 407 
 PHE   0.010   0.001   PHE A1040 
 TRP   0.007   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 ( 8031)
  covalent geometry    : angle       0.49259 /  0.25 (10899)
  SS BOND              : bond        0.00127 /  0.07 (    1)
  SS BOND              : angle       0.41680 /  0.24 (    2)
  hydrogen bonds       : bond        0.03397 /  2.24 (  403)
  hydrogen bonds       : angle       4.23070 /  2.91 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6000 (ptm-80)
REVERT: A  426 ASP cc_start: 0.7197 (t0) cc_final: 0.6833 (t0)
REVERT: A  479 MET cc_start: 0.6999 (tpt) cc_final: 0.6746 (tpt)
REVERT: A  482 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6066 (mp0)
REVERT: A  549 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6778 (mtm110)
REVERT: A  553 SER cc_start: 0.7994 (t) cc_final: 0.7752 (p)
REVERT: A  568 ASN cc_start: 0.7694 (t0) cc_final: 0.7443 (p0)
REVERT: A  585 LYS cc_start: 0.7826 (ptpp) cc_final: 0.7544 (pttp)
REVERT: A  763 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8611 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0845
  time to fit residues: 11.8860
Evaluate side-chains
  99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  763 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.179738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.105311 restraints weight = 8598.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.14
r_work: 0.2981 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8032  Z= 0.136
  Angle     :  0.515   8.117  10901  Z= 0.259
  Chirality :  0.042   0.200   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.743  24.006   1078
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.32 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.27), residues: 1014
  helix:  1.86 (0.23), residues: 501
  sheet: -0.36 (0.68), residues: 62
  loop : -0.30 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.018   0.002   TYR A 842 
 PHE   0.010   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 405 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 8031)
  covalent geometry    : angle       0.51545 /  0.26 (10899)
  SS BOND              : bond        0.00146 /  0.08 (    1)
  SS BOND              : angle       0.53421 /  0.31 (    2)
  hydrogen bonds       : bond        0.03724 /  2.45 (  403)
  hydrogen bonds       : angle       4.29935 /  2.96 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6043 (ptm-80)
REVERT: A  152 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5683 (pm20)
REVERT: A  426 ASP cc_start: 0.7243 (t0) cc_final: 0.6806 (t0)
REVERT: A  482 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.6034 (mp0)
REVERT: A  549 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.6656 (mtm110)
REVERT: A  553 SER cc_start: 0.7903 (t) cc_final: 0.7668 (p)
REVERT: A  568 ASN cc_start: 0.7708 (t0) cc_final: 0.7475 (p0)
REVERT: A  585 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7625 (pttp)
REVERT: A  693 PHE cc_start: 0.7743 (m-80) cc_final: 0.7516 (m-80)
REVERT: A  763 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8596 (mp)
  outliers start: 13
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0803
  time to fit residues: 11.6515
Evaluate side-chains
  105 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 82 optimal weight:    0.1980
   chunk 75 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.8184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.180698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.106989 restraints weight = 8547.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.27
r_work: 0.2972 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2834 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8032  Z= 0.113
  Angle     :  0.504   8.396  10901  Z= 0.254
  Chirality :  0.041   0.187   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.732  23.403   1078
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.55 %
    Favored  : 84.31 %
  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:  1.19 (0.27), residues: 1014
  helix:  1.91 (0.23), residues: 501
  sheet: -0.25 (0.70), residues: 62
  loop : -0.30 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 407 
 PHE   0.010   0.001   PHE A 367 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.11 ( 8031)
  covalent geometry    : angle       0.50410 /  0.25 (10899)
  SS BOND              : bond        0.00124 /  0.07 (    1)
  SS BOND              : angle       0.42159 /  0.24 (    2)
  hydrogen bonds       : bond        0.03543 /  2.33 (  403)
  hydrogen bonds       : angle       4.23488 /  2.91 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.5990 (ptm-80)
REVERT: A  152 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5749 (pm20)
REVERT: A  426 ASP cc_start: 0.7351 (t0) cc_final: 0.6869 (t0)
REVERT: A  482 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6040 (mp0)
REVERT: A  549 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.6694 (mtm110)
REVERT: A  553 SER cc_start: 0.8114 (t) cc_final: 0.7810 (p)
REVERT: A  568 ASN cc_start: 0.7663 (t0) cc_final: 0.7453 (p0)
REVERT: A  575 MET cc_start: 0.6894 (mmp) cc_final: 0.5312 (tmm)
REVERT: A  585 LYS cc_start: 0.7842 (ptpp) cc_final: 0.7564 (pttp)
REVERT: A  693 PHE cc_start: 0.7620 (m-80) cc_final: 0.7388 (m-80)
REVERT: A  763 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8632 (mp)
  outliers start: 10
  outliers final: 7
  residues processed: 101
  average time/residue: 0.0831
  time to fit residues: 12.0057
Evaluate side-chains
  99 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 80 optimal weight:    0.4980
   chunk 74 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.6382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.181354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.107114 restraints weight = 8488.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.08
r_work: 0.3012 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8032  Z= 0.104
  Angle     :  0.499   8.716  10901  Z= 0.250
  Chirality :  0.041   0.182   1279
  Planarity :  0.003   0.047   1389
  Dihedral  :  3.689  22.812   1078
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 14.55 %
    Favored  : 84.42 %
  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:  1.23 (0.27), residues: 1014
  helix:  1.95 (0.23), residues: 501
  sheet: -0.25 (0.70), residues: 62
  loop : -0.29 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 407 
 PHE   0.011   0.001   PHE A 367 
 TRP   0.006   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.10 ( 8031)
  covalent geometry    : angle       0.49855 /  0.25 (10899)
  SS BOND              : bond        0.00123 /  0.06 (    1)
  SS BOND              : angle       0.40243 /  0.23 (    2)
  hydrogen bonds       : bond        0.03394 /  2.24 (  403)
  hydrogen bonds       : angle       4.16703 /  2.87 ( 1185)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   58 GLU cc_start: 0.8095 (pp20) cc_final: 0.7819 (pp20)
REVERT: A  134 ARG cc_start: 0.6681 (mtm-85) cc_final: 0.5970 (ptm-80)
REVERT: A  239 MET cc_start: 0.4571 (mmm) cc_final: 0.4279 (mmm)
REVERT: A  426 ASP cc_start: 0.7240 (t0) cc_final: 0.6774 (t0)
REVERT: A  482 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6106 (mp0)
REVERT: A  549 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.6659 (mtm110)
REVERT: A  553 SER cc_start: 0.8057 (t) cc_final: 0.7772 (p)
REVERT: A  575 MET cc_start: 0.6856 (mmp) cc_final: 0.5290 (tmm)
REVERT: A  585 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7851 (pttp)
REVERT: A  693 PHE cc_start: 0.7537 (m-80) cc_final: 0.7264 (m-80)
REVERT: A  763 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (mp)
  outliers start: 9
  outliers final: 7
  residues processed: 97
  average time/residue: 0.0845
  time to fit residues: 11.7077
Evaluate side-chains
  100 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  495 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  663 SER
Chi-restraints excluded: chain A residue  763 LEU
Chi-restraints excluded: chain A residue  978 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 92 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.181385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.107850 restraints weight = 8493.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.02
r_work: 0.3013 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8032  Z= 0.108
  Angle     :  0.518   9.377  10901  Z= 0.258
  Chirality :  0.041   0.181   1279
  Planarity :  0.004   0.047   1389
  Dihedral  :  3.670  23.061   1078
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 14.09 %
    Favored  : 84.42 %
  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:  1.22 (0.27), residues: 1014
  helix:  1.95 (0.23), residues: 501
  sheet: -0.33 (0.69), residues: 62
  loop : -0.29 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 134 
 TYR   0.016   0.001   TYR A 407 
 PHE   0.011   0.001   PHE A 367 
 TRP   0.006   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.11 ( 8031)
  covalent geometry    : angle       0.51841 /  0.26 (10899)
  SS BOND              : bond        0.00128 /  0.07 (    1)
  SS BOND              : angle       0.40596 /  0.23 (    2)
  hydrogen bonds       : bond        0.03403 /  2.24 (  403)
  hydrogen bonds       : angle       4.14846 /  2.85 ( 1185)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2476.55 seconds
wall clock time: 43 minutes 7.04 seconds (2587.04 seconds total)