Starting phenix.real_space_refine
on Thu Mar  5 23:19:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zmd_14795/03_2026/7zmd_14795.map"
  }
  resolution = 2.93
  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=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9290 atoms to isotropic.
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
     S      40      5.16       5
     C    5883      2.51       5
     N    1575      2.21       5
     O    1796      1.98       5
     H    9106      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18400
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 9205
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 25, 'TRANS': 570}
    Chain: "B"
      Number of atoms: 9195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 9195
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 25, 'TRANS': 569}
  Time building chain proxies: 3.39, per 1000 atoms: 0.18
  Number of scatterers: 18400
  At special positions: 0
  Unit cell: (106.858, 119.554, 79.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     O    1796      8.00
     N    1575      7.00
     C    5883      6.00
     H    9106      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: 1.72
  Conformation dependent library (CDL) restraints added in 609.8 milliseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2198

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 13 sheets defined
      43.4% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 554 through 565
    Processing helix  chain 'A' and resid 608 through 613
    Processing helix  chain 'A' and resid 615 through 622
    Processing helix  chain 'A' and resid 623 through 640
    Processing helix  chain 'A' and resid 643 through 648
      removed outlier: 4.589A  pdb=" N   CYS A 648 " --> pdb=" O   PRO A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 681
      removed outlier: 4.123A  pdb=" N   ALA A 674 " --> pdb=" O   TYR A 670 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 677 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 694
      No H-bonds generated for 'chain 'A' and resid 692 through 694'
    Processing helix  chain 'A' and resid 695 through 710
    Processing helix  chain 'A' and resid 726 through 736
      removed outlier: 4.309A  pdb=" N   TYR A 730 " --> pdb=" O   ASP A 726 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU A 733 " --> pdb=" O   HIS A 729 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 736 " --> pdb=" O   LYS A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 776
    Processing helix  chain 'A' and resid 801 through 817
    Processing helix  chain 'A' and resid 819 through 821
      No H-bonds generated for 'chain 'A' and resid 819 through 821'
    Processing helix  chain 'A' and resid 835 through 850
      removed outlier: 3.829A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 868
    Processing helix  chain 'A' and resid 870 through 872
      No H-bonds generated for 'chain 'A' and resid 870 through 872'
    Processing helix  chain 'A' and resid 873 through 889
    Processing helix  chain 'A' and resid 905 through 909
    Processing helix  chain 'A' and resid 926 through 930
      removed outlier: 3.653A  pdb=" N   GLY A 929 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 983 through 1002
    Processing helix  chain 'A' and resid 1004 through 1006
      No H-bonds generated for 'chain 'A' and resid 1004 through 1006'
    Processing helix  chain 'A' and resid 1007 through 1018
    Processing helix  chain 'A' and resid 1032 through 1045
    Processing helix  chain 'A' and resid 1062 through 1071
      removed outlier: 4.025A  pdb=" N   ASP A1071 " --> pdb=" O   ILE A1067 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1084
      removed outlier: 4.170A  pdb=" N   GLU A1075 " --> pdb=" O   ASP A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1095
    Processing helix  chain 'A' and resid 1101 through 1106
      removed outlier: 3.609A  pdb=" N   LYS A1104 " --> pdb=" O   ASP A1101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 565
    Processing helix  chain 'B' and resid 608 through 613
    Processing helix  chain 'B' and resid 615 through 622
    Processing helix  chain 'B' and resid 623 through 640
    Processing helix  chain 'B' and resid 643 through 648
      removed outlier: 4.588A  pdb=" N   CYS B 648 " --> pdb=" O   PRO B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 681
      removed outlier: 4.122A  pdb=" N   ALA B 674 " --> pdb=" O   TYR B 670 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU B 677 " --> pdb=" O   ILE B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 694
      No H-bonds generated for 'chain 'B' and resid 692 through 694'
    Processing helix  chain 'B' and resid 695 through 710
    Processing helix  chain 'B' and resid 726 through 736
      removed outlier: 4.309A  pdb=" N   TYR B 730 " --> pdb=" O   ASP B 726 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU B 733 " --> pdb=" O   HIS B 729 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU B 736 " --> pdb=" O   LYS B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 776
    Processing helix  chain 'B' and resid 801 through 817
    Processing helix  chain 'B' and resid 819 through 821
      No H-bonds generated for 'chain 'B' and resid 819 through 821'
    Processing helix  chain 'B' and resid 835 through 850
      removed outlier: 3.829A  pdb=" N   ILE B 839 " --> pdb=" O   LEU B 835 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 863 through 868
    Processing helix  chain 'B' and resid 870 through 872
      No H-bonds generated for 'chain 'B' and resid 870 through 872'
    Processing helix  chain 'B' and resid 873 through 889
    Processing helix  chain 'B' and resid 905 through 909
    Processing helix  chain 'B' and resid 983 through 1002
    Processing helix  chain 'B' and resid 1004 through 1006
      No H-bonds generated for 'chain 'B' and resid 1004 through 1006'
    Processing helix  chain 'B' and resid 1007 through 1018
    Processing helix  chain 'B' and resid 1032 through 1045
    Processing helix  chain 'B' and resid 1062 through 1071
      removed outlier: 4.024A  pdb=" N   ASP B1071 " --> pdb=" O   ILE B1067 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1071 through 1084
      removed outlier: 4.169A  pdb=" N   GLU B1075 " --> pdb=" O   ASP B1071 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1086 through 1095
    Processing helix  chain 'B' and resid 1101 through 1106
      removed outlier: 3.609A  pdb=" N   LYS B1104 " --> pdb=" O   ASP B1101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 823 through 827
      removed outlier: 6.926A  pdb=" N   ILE A 937 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR A 825 " --> pdb=" O   ILE A 937 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ASN A 949 " --> pdb=" O   MET A 788 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   MET A 788 " --> pdb=" O   ASN A 949 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   HIS A 951 " --> pdb=" O   SER A 786 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER A 786 " --> pdb=" O   HIS A 951 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ILE A 953 " --> pdb=" O   LYS A 784 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLY A 781 " --> pdb=" O   ILE A 542 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL A 765 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LEU A 545 " --> pdb=" O   ALA A 763 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   ALA A 763 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 761 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A 761 " --> pdb=" O   GLY A 547 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   VAL A 688 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL A 655 " --> pdb=" O   VAL A 688 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   VAL A 690 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL A 657 " --> pdb=" O   VAL A 690 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   VAL B 688 " --> pdb=" O   VAL B 653 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   VAL B 655 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   VAL B 690 " --> pdb=" O   VAL B 655 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL B 657 " --> pdb=" O   VAL B 690 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL B 761 " --> pdb=" O   GLY B 547 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   GLY B 547 " --> pdb=" O   VAL B 761 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ALA B 763 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   LEU B 545 " --> pdb=" O   ALA B 763 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL B 765 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY B 781 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ILE B 953 " --> pdb=" O   LYS B 784 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   SER B 786 " --> pdb=" O   HIS B 951 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   HIS B 951 " --> pdb=" O   SER B 786 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET B 788 " --> pdb=" O   ASN B 949 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ASN B 949 " --> pdb=" O   MET B 788 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ILE B 937 " --> pdb=" O   VAL B 823 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR B 825 " --> pdb=" O   ILE B 937 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 571
    Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607
    Processing sheet with id=AA4, first strand: chain 'A' and resid 858 through 860
      removed outlier: 6.209A  pdb=" N   CYS A 858 " --> pdb=" O   VAL A 912 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891
    Processing sheet with id=AA6, first strand: chain 'A' and resid 924 through 925
      removed outlier: 3.567A  pdb=" N   VAL A 925 " --> pdb=" O   ASN A 932 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 975 through 981
      removed outlier: 3.505A  pdb=" N   ALA A1030 " --> pdb=" O   ALA A 975 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A1056 " --> pdb=" O   ARG A1025 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A1027 " --> pdb=" O   TYR A1054 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 570 through 571
    Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 607
    Processing sheet with id=AB1, first strand: chain 'B' and resid 858 through 860
      removed outlier: 6.209A  pdb=" N   CYS B 858 " --> pdb=" O   VAL B 912 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 890 through 891
    Processing sheet with id=AB3, first strand: chain 'B' and resid 924 through 925
      removed outlier: 3.566A  pdb=" N   VAL B 925 " --> pdb=" O   ASN B 932 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 975 through 981
      removed outlier: 3.504A  pdb=" N   ALA B1030 " --> pdb=" O   ALA B 975 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY B1056 " --> pdb=" O   ARG B1025 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA B1027 " --> pdb=" O   TYR B1054 " (cutoff:3.500A)

    407 hydrogen bonds defined for protein.
    1128 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.82

  Time building geometry restraints manager: 2.40 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: 9094
        1.03 -     1.23: 12
        1.23 -     1.42: 3993
        1.42 -     1.62: 5435
        1.62 -     1.81: 66
  Bond restraints: 18600
  Sorted by residual:
  bond pdb=" CD  ARG B1025 "
       pdb=" NE  ARG B1025 "
    ideal  model  delta    sigma   weight residual
    1.458  1.444  0.014 1.40e-02 5.10e+03 9.67e-01
  bond pdb=" NH1 ARG A1025 "
       pdb="HH12 ARG A1025 "
    ideal  model  delta    sigma   weight residual
    0.860  0.840  0.020 2.00e-02 2.50e+03 9.60e-01
  bond pdb=" CD  ARG A1025 "
       pdb=" NE  ARG A1025 "
    ideal  model  delta    sigma   weight residual
    1.458  1.445  0.013 1.40e-02 5.10e+03 9.14e-01
  bond pdb=" C   TYR A 664 "
       pdb=" N   PRO A 665 "
    ideal  model  delta    sigma   weight residual
    1.336  1.346 -0.010 1.08e-02 8.57e+03 9.06e-01
  bond pdb=" C   TYR B 664 "
       pdb=" N   PRO B 665 "
    ideal  model  delta    sigma   weight residual
    1.336  1.346 -0.010 1.08e-02 8.57e+03 8.84e-01
  ... (remaining 18595 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.52: 33582
        7.52 -    15.05: 6
       15.05 -    22.57: 1
       22.57 -    30.10: 14
       30.10 -    37.62: 11
  Bond angle restraints: 33614
  Sorted by residual:
  angle pdb=" N   VAL A 536 "
        pdb=" CA  VAL A 536 "
        pdb=" HA  VAL A 536 "
      ideal   model   delta    sigma   weight residual
     110.00   72.38   37.62 3.00e+00 1.11e-01 1.57e+02
  angle pdb=" C   VAL A 536 "
        pdb=" CA  VAL A 536 "
        pdb=" HA  VAL A 536 "
      ideal   model   delta    sigma   weight residual
     109.00   71.69   37.31 3.00e+00 1.11e-01 1.55e+02
  angle pdb=" OG1 THR A 699 "
        pdb=" CB  THR A 699 "
        pdb=" HB  THR A 699 "
      ideal   model   delta    sigma   weight residual
     109.00   74.04   34.96 3.00e+00 1.11e-01 1.36e+02
  angle pdb=" CG2 THR A 699 "
        pdb=" CB  THR A 699 "
        pdb=" HB  THR A 699 "
      ideal   model   delta    sigma   weight residual
     108.00   73.69   34.31 3.00e+00 1.11e-01 1.31e+02
  angle pdb=" OG1 THR A 669 "
        pdb=" CB  THR A 669 "
        pdb=" HB  THR A 669 "
      ideal   model   delta    sigma   weight residual
     109.00   75.45   33.55 3.00e+00 1.11e-01 1.25e+02
  ... (remaining 33609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.90: 7936
       15.90 -    31.80: 567
       31.80 -    47.70: 161
       47.70 -    63.60: 87
       63.60 -    79.50: 16
  Dihedral angle restraints: 8767
    sinusoidal: 4750
      harmonic: 4017
  Sorted by residual:
  dihedral pdb=" CD  ARG B1025 "
           pdb=" NE  ARG B1025 "
           pdb=" CZ  ARG B1025 "
           pdb=" NH1 ARG B1025 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   51.82  -51.82     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CD  ARG A1025 "
           pdb=" NE  ARG A1025 "
           pdb=" CZ  ARG A1025 "
           pdb=" NH1 ARG A1025 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   51.80  -51.80     1      1.00e+01 1.00e-02 3.66e+01
  dihedral pdb=" CA  LEU B 736 "
           pdb=" C   LEU B 736 "
           pdb=" N   THR B 737 "
           pdb=" CA  THR B 737 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.34   19.66     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 8764 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.342: 1405
       0.342 -    0.684: 4
       0.684 -    1.026: 0
       1.026 -    1.368: 0
       1.368 -    1.710: 2
  Chirality restraints: 1411
  Sorted by residual:
  chirality pdb=" CG  LEU A 826 "
            pdb=" CB  LEU A 826 "
            pdb=" CD1 LEU A 826 "
            pdb=" CD2 LEU A 826 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.88   -1.71 2.00e-01 2.50e+01 7.31e+01
  chirality pdb=" CG  LEU B 826 "
            pdb=" CB  LEU B 826 "
            pdb=" CD1 LEU B 826 "
            pdb=" CD2 LEU B 826 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.88   -1.71 2.00e-01 2.50e+01 7.27e+01
  chirality pdb=" CB  THR B 699 "
            pdb=" CA  THR B 699 "
            pdb=" OG1 THR B 699 "
            pdb=" CG2 THR B 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.03    0.52 2.00e-01 2.50e+01 6.71e+00
  ... (remaining 1408 not shown)

  Planarity restraints: 2818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1025 "   -0.820 9.50e-02 1.11e+02   2.74e-01 8.62e+01
        pdb=" NE  ARG A1025 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1025 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1025 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1025 "   -0.012 2.00e-02 2.50e+03
        pdb="HH11 ARG A1025 "   -0.006 2.00e-02 2.50e+03
        pdb="HH12 ARG A1025 "    0.023 2.00e-02 2.50e+03
        pdb="HH21 ARG A1025 "   -0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A1025 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B1025 "   -0.835 9.50e-02 1.11e+02   2.79e-01 8.52e+01
        pdb=" NE  ARG B1025 "    0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG B1025 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B1025 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG B1025 "   -0.008 2.00e-02 2.50e+03
        pdb="HH11 ARG B1025 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG B1025 "    0.013 2.00e-02 2.50e+03
        pdb="HH21 ARG B1025 "   -0.004 2.00e-02 2.50e+03
        pdb="HH22 ARG B1025 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 767 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.16e+00
        pdb=" N   PRO B 768 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 768 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 768 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2815 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 535
        2.14 -     2.76: 34481
        2.76 -     3.37: 51267
        3.37 -     3.99: 67559
        3.99 -     4.60: 107523
  Nonbonded interactions: 261365
  Sorted by model distance:
  nonbonded pdb="HH21 ARG B 986 "
            pdb=" OE2 GLU B 989 "
     model   vdw
     1.531 2.450
  nonbonded pdb="HH21 ARG A 986 "
            pdb=" OE2 GLU A 989 "
     model   vdw
     1.531 2.450
  nonbonded pdb=" HE3 LYS A1086 "
            pdb=" HZ2 LYS A1086 "
     model   vdw
     1.598 1.816
  nonbonded pdb=" HE2 LYS A1086 "
            pdb=" HZ3 LYS A1086 "
     model   vdw
     1.599 1.816
  nonbonded pdb=" HB  THR A 669 "
            pdb="HG23 THR A 669 "
     model   vdw
     1.628 1.952
  ... (remaining 261360 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 536 through 1130)
  selection = chain 'B'
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     18.700
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:8.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
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      :  0.002   0.030   9494  Z= 0.095
  Angle     :  0.522  10.126  12870  Z= 0.261
  Chirality :  0.081   1.710   1411
  Planarity :  0.013   0.370   1681
  Dihedral  : 13.129  79.496   3486
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  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 (0.25), residues: 1187
  helix:  1.91 (0.25), residues: 412
  sheet:  0.95 (0.46), residues: 138
  loop : -0.30 (0.25), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1025 
 TYR   0.008   0.001   TYR B 642 
 PHE   0.006   0.001   PHE B 857 
 TRP   0.006   0.001   TRP A1081 
 HIS   0.004   0.001   HIS A1049 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 9494)
  covalent geometry    : angle       0.52243 (12870)
  hydrogen bonds       : bond        0.17796 (  407)
  hydrogen bonds       : angle       6.68009 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  854 ASP cc_start: 0.7711 (m-30) cc_final: 0.7366 (m-30)
REVERT: B  854 ASP cc_start: 0.7772 (m-30) cc_final: 0.7416 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 1.4763
  time to fit residues: 225.0018
Evaluate side-chains
  98 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 853 GLN
A 856 GLN
A1037 GLN
A1110 GLN
B 853 GLN
B 856 GLN
B1110 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.161276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132956 restraints weight = 28483.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.66
r_work: 0.3378 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   9494  Z= 0.243
  Angle     :  0.704  24.738  12870  Z= 0.356
  Chirality :  0.095   1.748   1411
  Planarity :  0.005   0.050   1681
  Dihedral  :  4.549  22.599   1277
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.89 %
    Favored  : 89.30 %
  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 (0.24), residues: 1187
  helix:  1.38 (0.24), residues: 420
  sheet:  0.27 (0.41), residues: 164
  loop : -0.47 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1025 
 TYR   0.016   0.002   TYR A 642 
 PHE   0.017   0.002   PHE B 911 
 TRP   0.011   0.002   TRP B 920 
 HIS   0.004   0.001   HIS B 702 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 9494)
  covalent geometry    : angle       0.70400 (12870)
  hydrogen bonds       : bond        0.05676 (  407)
  hydrogen bonds       : angle       5.00302 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  854 ASP cc_start: 0.8182 (m-30) cc_final: 0.7760 (m-30)
REVERT: A  926 GLU cc_start: 0.7288 (tm-30) cc_final: 0.7015 (tm-30)
REVERT: B  854 ASP cc_start: 0.8142 (m-30) cc_final: 0.7724 (m-30)
REVERT: B  926 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: B 1103 ASN cc_start: 0.8677 (m-40) cc_final: 0.8460 (m-40)
  outliers start: 8
  outliers final: 4
  residues processed: 122
  average time/residue: 1.4062
  time to fit residues: 182.1056
Evaluate side-chains
  108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  931 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 853 GLN
B 751 GLN
B 853 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.161123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.133956 restraints weight = 28579.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 1.62
r_work: 0.3405 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9494  Z= 0.149
  Angle     :  0.622  25.447  12870  Z= 0.304
  Chirality :  0.094   1.754   1411
  Planarity :  0.004   0.040   1681
  Dihedral  :  4.202  20.448   1277
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.91 %
    Favored  : 87.18 %
  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:  0.49 (0.24), residues: 1187
  helix:  1.47 (0.25), residues: 424
  sheet:  0.61 (0.44), residues: 144
  loop : -0.54 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1025 
 TYR   0.010   0.001   TYR A 988 
 PHE   0.011   0.001   PHE B 629 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.003   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9494)
  covalent geometry    : angle       0.62218 (12870)
  hydrogen bonds       : bond        0.04760 (  407)
  hydrogen bonds       : angle       4.74046 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  850 LYS cc_start: 0.7594 (tttt) cc_final: 0.6698 (mttt)
REVERT: A  854 ASP cc_start: 0.8202 (m-30) cc_final: 0.7790 (m-30)
REVERT: A  926 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6889 (tm-30)
REVERT: A 1048 GLU cc_start: 0.6609 (pp20) cc_final: 0.6297 (pp20)
REVERT: B  850 LYS cc_start: 0.7616 (tttt) cc_final: 0.6692 (mttt)
REVERT: B  854 ASP cc_start: 0.8143 (m-30) cc_final: 0.7768 (m-30)
REVERT: B  926 GLU cc_start: 0.7277 (tm-30) cc_final: 0.7051 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 114
  average time/residue: 1.3679
  time to fit residues: 166.2087
Evaluate side-chains
  102 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  931 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 751 GLN
A 853 GLN
A 999 GLN
B 751 GLN
B 817 ASN
B 999 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.160361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.134007 restraints weight = 29213.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.57
r_work: 0.3399 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9494  Z= 0.162
  Angle     :  0.637  25.978  12870  Z= 0.311
  Chirality :  0.096   1.753   1411
  Planarity :  0.004   0.042   1681
  Dihedral  :  4.230  19.921   1277
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.71 %
    Favored  : 87.18 %
  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:  0.37 (0.24), residues: 1187
  helix:  1.38 (0.24), residues: 428
  sheet:  0.47 (0.44), residues: 150
  loop : -0.61 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B1025 
 TYR   0.008   0.001   TYR A 988 
 PHE   0.012   0.002   PHE B 629 
 TRP   0.006   0.001   TRP B1102 
 HIS   0.003   0.001   HIS A 729 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 9494)
  covalent geometry    : angle       0.63668 (12870)
  hydrogen bonds       : bond        0.04565 (  407)
  hydrogen bonds       : angle       4.60090 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  850 LYS cc_start: 0.7459 (tttt) cc_final: 0.6522 (mtmt)
REVERT: A  854 ASP cc_start: 0.8158 (m-30) cc_final: 0.7783 (m-30)
REVERT: A  926 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6833 (tm-30)
REVERT: A 1092 ASP cc_start: 0.7835 (t0) cc_final: 0.7622 (t0)
REVERT: B  787 MET cc_start: 0.8894 (tpp) cc_final: 0.8693 (tpp)
REVERT: B  850 LYS cc_start: 0.7492 (tttt) cc_final: 0.6548 (mtmt)
REVERT: B  854 ASP cc_start: 0.8141 (m-30) cc_final: 0.7766 (m-30)
REVERT: B  926 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6801 (tm-30)
REVERT: B 1103 ASN cc_start: 0.8723 (m-40) cc_final: 0.8476 (m-40)
  outliers start: 11
  outliers final: 5
  residues processed: 107
  average time/residue: 1.4358
  time to fit residues: 163.3006
Evaluate side-chains
  100 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  925 VAL
Chi-restraints excluded: chain B residue  931 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 817 ASN
A 999 GLN
A1103 ASN
B 999 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.157969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.130739 restraints weight = 29216.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 1.64
r_work: 0.3356 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9494  Z= 0.214
  Angle     :  0.679  26.172  12870  Z= 0.334
  Chirality :  0.097   1.785   1411
  Planarity :  0.005   0.044   1681
  Dihedral  :  4.475  18.930   1277
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.40 %
    Favored  : 86.78 %
  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:  0.06 (0.24), residues: 1187
  helix:  1.16 (0.24), residues: 428
  sheet:  0.11 (0.41), residues: 163
  loop : -0.80 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1025 
 TYR   0.010   0.002   TYR A 642 
 PHE   0.012   0.002   PHE B 629 
 TRP   0.008   0.001   TRP A1102 
 HIS   0.004   0.001   HIS A 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 9494)
  covalent geometry    : angle       0.67852 (12870)
  hydrogen bonds       : bond        0.05182 (  407)
  hydrogen bonds       : angle       4.67567 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  807 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7920 (tp40)
REVERT: A  850 LYS cc_start: 0.7503 (tttt) cc_final: 0.6574 (mtmt)
REVERT: A  854 ASP cc_start: 0.8139 (m-30) cc_final: 0.7755 (m-30)
REVERT: A  926 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6810 (tm-30)
REVERT: A 1044 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7158 (t)
REVERT: A 1055 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6865 (mtt-85)
REVERT: B  807 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7920 (tp40)
REVERT: B  850 LYS cc_start: 0.7512 (tttt) cc_final: 0.6565 (mtmt)
REVERT: B  854 ASP cc_start: 0.8178 (m-30) cc_final: 0.7843 (m-30)
REVERT: B  926 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6826 (tm-30)
REVERT: B 1044 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7110 (t)
REVERT: B 1055 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6855 (mtt-85)
  outliers start: 18
  outliers final: 7
  residues processed: 113
  average time/residue: 1.5434
  time to fit residues: 184.6842
Evaluate side-chains
  111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  610 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  931 THR
Chi-restraints excluded: chain B residue 1044 VAL
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 999 GLN
B 817 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.158343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.131299 restraints weight = 28472.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 1.62
r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9494  Z= 0.146
  Angle     :  0.630  26.213  12870  Z= 0.305
  Chirality :  0.095   1.762   1411
  Planarity :  0.004   0.044   1681
  Dihedral  :  4.258  18.968   1277
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.81 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.24), residues: 1187
  helix:  1.31 (0.24), residues: 428
  sheet: -0.02 (0.41), residues: 164
  loop : -0.68 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 986 
 TYR   0.008   0.001   TYR A 988 
 PHE   0.011   0.001   PHE A 629 
 TRP   0.006   0.001   TRP B 559 
 HIS   0.002   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9494)
  covalent geometry    : angle       0.62958 (12870)
  hydrogen bonds       : bond        0.04381 (  407)
  hydrogen bonds       : angle       4.53742 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  850 LYS cc_start: 0.7480 (tttt) cc_final: 0.6510 (ttmt)
REVERT: A  854 ASP cc_start: 0.8138 (m-30) cc_final: 0.7806 (m-30)
REVERT: A  926 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6773 (tm-30)
REVERT: A 1055 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6804 (mtt-85)
REVERT: B  770 ASP cc_start: 0.8115 (p0) cc_final: 0.7803 (p0)
REVERT: B  850 LYS cc_start: 0.7477 (tttt) cc_final: 0.6507 (ttmt)
REVERT: B  854 ASP cc_start: 0.8119 (m-30) cc_final: 0.7788 (m-30)
REVERT: B  926 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6840 (tm-30)
REVERT: B 1055 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6770 (mtt-85)
REVERT: B 1103 ASN cc_start: 0.8666 (m-40) cc_final: 0.8404 (m-40)
  outliers start: 9
  outliers final: 6
  residues processed: 111
  average time/residue: 1.5358
  time to fit residues: 179.9402
Evaluate side-chains
  104 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  931 THR
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 817 ASN
A 999 GLN
B 751 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.160179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.133201 restraints weight = 29278.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 1.63
r_work: 0.3388 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9494  Z= 0.129
  Angle     :  0.609  26.098  12870  Z= 0.294
  Chirality :  0.095   1.755   1411
  Planarity :  0.004   0.045   1681
  Dihedral  :  4.102  18.840   1277
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.21 %
    Favored  : 86.58 %
  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 (0.24), residues: 1187
  helix:  1.49 (0.24), residues: 428
  sheet: -0.02 (0.40), residues: 164
  loop : -0.64 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1025 
 TYR   0.007   0.001   TYR B 988 
 PHE   0.011   0.001   PHE A 629 
 TRP   0.006   0.001   TRP A 559 
 HIS   0.002   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9494)
  covalent geometry    : angle       0.60926 (12870)
  hydrogen bonds       : bond        0.04117 (  407)
  hydrogen bonds       : angle       4.46761 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  770 ASP cc_start: 0.8093 (p0) cc_final: 0.7786 (p0)
REVERT: A  850 LYS cc_start: 0.7399 (tttt) cc_final: 0.6479 (ttmt)
REVERT: A  854 ASP cc_start: 0.8108 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  926 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6858 (tm-30)
REVERT: A 1055 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6731 (mtt-85)
REVERT: B  770 ASP cc_start: 0.8030 (p0) cc_final: 0.7700 (p0)
REVERT: B  850 LYS cc_start: 0.7341 (tttt) cc_final: 0.6307 (mttt)
REVERT: B  854 ASP cc_start: 0.8077 (m-30) cc_final: 0.7776 (m-30)
REVERT: B  926 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6703 (tm-30)
REVERT: B 1044 VAL cc_start: 0.7491 (OUTLIER) cc_final: 0.7137 (t)
REVERT: B 1055 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6708 (mtt-85)
  outliers start: 12
  outliers final: 5
  residues processed: 113
  average time/residue: 1.5343
  time to fit residues: 183.3482
Evaluate side-chains
  108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  925 VAL
Chi-restraints excluded: chain B residue 1044 VAL
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 999 GLN
B 817 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.154790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.126377 restraints weight = 29559.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.73
r_work: 0.3384 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9494  Z= 0.143
  Angle     :  0.618  26.174  12870  Z= 0.300
  Chirality :  0.095   1.761   1411
  Planarity :  0.004   0.045   1681
  Dihedral  :  4.103  18.596   1277
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.22 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.35 (0.24), residues: 1187
  helix:  1.55 (0.24), residues: 428
  sheet:  0.04 (0.41), residues: 164
  loop : -0.67 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1025 
 TYR   0.008   0.001   TYR B 988 
 PHE   0.012   0.001   PHE A 629 
 TRP   0.006   0.001   TRP B 559 
 HIS   0.004   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9494)
  covalent geometry    : angle       0.61832 (12870)
  hydrogen bonds       : bond        0.04264 (  407)
  hydrogen bonds       : angle       4.46779 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  621 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7749 (mp0)
REVERT: A  770 ASP cc_start: 0.7982 (p0) cc_final: 0.7653 (p0)
REVERT: A  850 LYS cc_start: 0.7302 (tttt) cc_final: 0.6203 (mttt)
REVERT: A  854 ASP cc_start: 0.8144 (m-30) cc_final: 0.7817 (m-30)
REVERT: A  926 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6753 (tm-30)
REVERT: A 1044 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.6913 (t)
REVERT: A 1055 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6654 (mtt-85)
REVERT: B  850 LYS cc_start: 0.7283 (tttt) cc_final: 0.6181 (mttt)
REVERT: B  854 ASP cc_start: 0.8059 (m-30) cc_final: 0.7774 (m-30)
REVERT: B  926 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6509 (tm-30)
REVERT: B 1044 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.6946 (t)
REVERT: B 1055 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6667 (mtt-85)
REVERT: B 1103 ASN cc_start: 0.8631 (m-40) cc_final: 0.8351 (m-40)
  outliers start: 12
  outliers final: 6
  residues processed: 110
  average time/residue: 1.5134
  time to fit residues: 176.3589
Evaluate side-chains
  107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  621 GLU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  777 ASP
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  925 VAL
Chi-restraints excluded: chain B residue 1044 VAL
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 817 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.159595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132510 restraints weight = 28944.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 1.64
r_work: 0.3381 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9494  Z= 0.141
  Angle     :  0.617  26.193  12870  Z= 0.299
  Chirality :  0.095   1.763   1411
  Planarity :  0.004   0.048   1681
  Dihedral  :  4.079  18.607   1277
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.03 %
    Favored  : 84.86 %
  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:  0.34 (0.24), residues: 1187
  helix:  1.60 (0.24), residues: 428
  sheet: -0.06 (0.39), residues: 174
  loop : -0.71 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1025 
 TYR   0.009   0.001   TYR A 988 
 PHE   0.011   0.001   PHE B 629 
 TRP   0.006   0.001   TRP B 559 
 HIS   0.003   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 9494)
  covalent geometry    : angle       0.61739 (12870)
  hydrogen bonds       : bond        0.04223 (  407)
  hydrogen bonds       : angle       4.45381 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  850 LYS cc_start: 0.7370 (tttt) cc_final: 0.6416 (ttmt)
REVERT: A  854 ASP cc_start: 0.8146 (m-30) cc_final: 0.7831 (m-30)
REVERT: A  926 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6831 (tm-30)
REVERT: A 1044 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7096 (t)
REVERT: A 1055 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6640 (mtt-85)
REVERT: B  850 LYS cc_start: 0.7347 (tttt) cc_final: 0.6389 (ttmt)
REVERT: B  854 ASP cc_start: 0.8091 (m-30) cc_final: 0.7803 (m-30)
REVERT: B  926 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6682 (tm-30)
REVERT: B 1044 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7123 (t)
REVERT: B 1048 GLU cc_start: 0.6368 (pp20) cc_final: 0.5963 (pp20)
REVERT: B 1055 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6653 (mtt-85)
REVERT: B 1088 SER cc_start: 0.8243 (t) cc_final: 0.7755 (p)
REVERT: B 1103 ASN cc_start: 0.8632 (m-40) cc_final: 0.8374 (m-40)
  outliers start: 11
  outliers final: 5
  residues processed: 105
  average time/residue: 1.5162
  time to fit residues: 168.6147
Evaluate side-chains
  107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1044 VAL
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  736 LEU
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  925 VAL
Chi-restraints excluded: chain B residue 1044 VAL
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0570
   chunk 6 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 795 ASN
A 999 GLN
B 751 GLN
B 817 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.159982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132975 restraints weight = 28613.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.63
r_work: 0.3399 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9494  Z= 0.111
  Angle     :  0.597  26.135  12870  Z= 0.287
  Chirality :  0.094   1.750   1411
  Planarity :  0.004   0.046   1681
  Dihedral  :  3.919  18.424   1277
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 14.23 %
    Favored  : 84.86 %
  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:  0.51 (0.24), residues: 1187
  helix:  1.78 (0.24), residues: 428
  sheet:  0.12 (0.40), residues: 165
  loop : -0.66 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 986 
 TYR   0.008   0.001   TYR A 642 
 PHE   0.010   0.001   PHE A 629 
 TRP   0.008   0.001   TRP B 559 
 HIS   0.003   0.001   HIS B 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9494)
  covalent geometry    : angle       0.59735 (12870)
  hydrogen bonds       : bond        0.03783 (  407)
  hydrogen bonds       : angle       4.37898 ( 1128)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  850 LYS cc_start: 0.7300 (tttt) cc_final: 0.6289 (ttmt)
REVERT: A  854 ASP cc_start: 0.8106 (m-30) cc_final: 0.7811 (m-30)
REVERT: A  926 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6758 (tm-30)
REVERT: A 1055 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6614 (mtt-85)
REVERT: B  850 LYS cc_start: 0.7285 (tttt) cc_final: 0.6274 (ttmt)
REVERT: B  854 ASP cc_start: 0.8082 (m-30) cc_final: 0.7804 (m-30)
REVERT: B  926 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: B 1048 GLU cc_start: 0.6366 (pp20) cc_final: 0.5943 (pp20)
REVERT: B 1055 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6645 (mtt-85)
REVERT: B 1103 ASN cc_start: 0.8643 (m-40) cc_final: 0.8394 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 110
  average time/residue: 1.4797
  time to fit residues: 172.7011
Evaluate side-chains
  103 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1055 ARG
Chi-restraints excluded: chain B residue  826 LEU
Chi-restraints excluded: chain B residue  925 VAL
Chi-restraints excluded: chain B residue 1055 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 109 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 817 ASN
A 999 GLN
B 999 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.161138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.134394 restraints weight = 29168.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.62
r_work: 0.3406 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9494  Z= 0.112
  Angle     :  0.598  26.122  12870  Z= 0.287
  Chirality :  0.094   1.745   1411
  Planarity :  0.004   0.047   1681
  Dihedral  :  3.873  18.752   1277
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 14.53 %
    Favored  : 84.86 %
  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:  0.57 (0.24), residues: 1187
  helix:  1.87 (0.25), residues: 428
  sheet:  0.13 (0.40), residues: 165
  loop : -0.65 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 986 
 TYR   0.008   0.001   TYR A 988 
 PHE   0.010   0.001   PHE B 629 
 TRP   0.007   0.001   TRP B 559 
 HIS   0.003   0.001   HIS A 869 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9494)
  covalent geometry    : angle       0.59834 (12870)
  hydrogen bonds       : bond        0.03794 (  407)
  hydrogen bonds       : angle       4.34799 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5941.81 seconds
wall clock time: 100 minutes 54.51 seconds (6054.51 seconds total)