Starting phenix.real_space_refine
on Thu Mar 13 15:13:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xci_38244/03_2025/8xci_38244.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.047
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: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    5603      2.51       5
     N    1501      2.21       5
     O    1723      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8842
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "F"
      Number of atoms: 2941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 2941
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 16, 'TRANS': 363}
    Chain: "J"
      Number of atoms: 2941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 2941
          Classifications: {'peptide': 380}
          Link IDs: {'PTRANS': 16, 'TRANS': 363}
    Chain: "Z"
      Number of atoms: 2960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 2960
          Classifications: {'peptide': 383}
          Link IDs: {'PTRANS': 16, 'TRANS': 366}
  Time building chain proxies: 5.85, per 1000 atoms: 0.66
  Number of scatterers: 8842
  At special positions: 0
  Unit cell: (128.904, 135.349, 107.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O    1723      8.00
     N    1501      7.00
     C    5603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.17
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 25 sheets defined
      7.6% alpha, 37.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'F' and resid 755 through 759
      removed outlier: 3.827A  pdb=" N   GLN F 758 " --> pdb=" O   ASP F 755 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 815 through 824
    Processing helix  chain 'F' and resid 825 through 831
    Processing helix  chain 'F' and resid 907 through 911
    Processing helix  chain 'J' and resid 758 through 763
    Processing helix  chain 'J' and resid 810 through 824
      removed outlier: 3.901A  pdb=" N   TYR J 814 " --> pdb=" O   ASP J 810 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 825 through 832
    Processing helix  chain 'Z' and resid 758 through 763
      removed outlier: 3.622A  pdb=" N   THR Z 763 " --> pdb=" O   VAL Z 759 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 811 through 824
      removed outlier: 3.877A  pdb=" N   ASP Z 816 " --> pdb=" O   GLU Z 812 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   PHE Z 817 " --> pdb=" O   GLY Z 813 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLU Z 824 " --> pdb=" O   GLY Z 820 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 827 through 832
      removed outlier: 3.633A  pdb=" N   LEU Z 832 " --> pdb=" O   GLY Z 828 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 907 through 911
    Processing sheet with id=AA1, first strand: chain 'F' and resid 636 through 640
    Processing sheet with id=AA2, first strand: chain 'F' and resid 665 through 673
      removed outlier: 5.646A  pdb=" N   LEU F 667 " --> pdb=" O   VAL F 658 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   VAL F 658 " --> pdb=" O   LEU F 667 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   ASN F 687 " --> pdb=" O   THR F 659 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 717 through 725
    Processing sheet with id=AA4, first strand: chain 'F' and resid 764 through 769
      removed outlier: 5.357A  pdb=" N   TYR F 765 " --> pdb=" O   PHE F 748 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE F 748 " --> pdb=" O   TYR F 765 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 842 through 848
      removed outlier: 6.226A  pdb=" N   PHE F 895 " --> pdb=" O   ALA Z 903 " (cutoff:3.500A)
      removed outlier: 8.163A  pdb=" N   ILE Z 905 " --> pdb=" O   PHE F 895 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL F 897 " --> pdb=" O   ILE Z 905 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE Z 904 " --> pdb=" O   PHE Z 916 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE Z 916 " --> pdb=" O   PHE Z 904 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 852 through 853
    Processing sheet with id=AA7, first strand: chain 'F' and resid 885 through 886
      removed outlier: 3.636A  pdb=" N   LEU F 892 " --> pdb=" O   GLU F 885 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'J' and resid 843 through 854
      removed outlier: 3.735A  pdb=" N   LYS J 858 " --> pdb=" O   ASP J 854 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 843 through 854
      removed outlier: 3.735A  pdb=" N   LYS J 858 " --> pdb=" O   ASP J 854 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU J 882 " --> pdb=" O   TRP J 863 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ARG F 901 " --> pdb=" O   PHE J 895 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   VAL J 897 " --> pdb=" O   ARG F 901 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ALA F 903 " --> pdb=" O   VAL J 897 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   PHE F 916 " --> pdb=" O   PHE F 904 " (cutoff:3.500A)
      removed outlier: 8.708A  pdb=" N   MET F 915 " --> pdb=" O   ASN F 926 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   PHE F 924 " --> pdb=" O   PHE Z 929 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   LYS Z 931 " --> pdb=" O   PHE F 924 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ASN F 926 " --> pdb=" O   LYS Z 931 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   THR J 934 " --> pdb=" O   LEU Z 930 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ARG Z 932 " --> pdb=" O   THR J 934 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 932 through 934
      removed outlier: 6.071A  pdb=" N   ARG F 932 " --> pdb=" O   VAL J 928 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 955 through 957
    Processing sheet with id=AB3, first strand: chain 'F' and resid 961 through 965
      removed outlier: 3.952A  pdb=" N   ALA J 957 " --> pdb=" O   ASP F 961 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ASN J 959 " --> pdb=" O   SER F 963 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   SER F 965 " --> pdb=" O   ASN J 959 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   SER J 948 " --> pdb=" O   THR J 956 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'J' and resid 970 through 971
      removed outlier: 6.539A  pdb=" N   ASN F 975 " --> pdb=" O   GLY J 971 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   ARG J 989 " --> pdb=" O   ILE Z 984 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   GLY Z 986 " --> pdb=" O   ARG J 989 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   GLU J 991 " --> pdb=" O   GLY Z 986 " (cutoff:3.500A)
      removed outlier: 7.931A  pdb=" N   LEU Z 988 " --> pdb=" O   GLU J 991 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ILE J 993 " --> pdb=" O   LEU Z 988 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 983 through 984
      removed outlier: 6.138A  pdb=" N   THR F 983 " --> pdb=" O   ILE J 978 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'F' and resid 987 through 988
    Processing sheet with id=AB7, first strand: chain 'J' and resid 622 through 629
      removed outlier: 5.403A  pdb=" N   HIS J 623 " --> pdb=" O   ASP J 642 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   ASP J 642 " --> pdb=" O   HIS J 623 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'J' and resid 665 through 673
      removed outlier: 5.646A  pdb=" N   LEU J 667 " --> pdb=" O   VAL J 658 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL J 658 " --> pdb=" O   LEU J 667 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   TYR J 688 " --> pdb=" O   SER J 708 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   SER J 708 " --> pdb=" O   TYR J 688 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   LEU J 690 " --> pdb=" O   SER J 706 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   SER J 706 " --> pdb=" O   LEU J 690 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL J 692 " --> pdb=" O   PRO J 704 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   ALA J 694 " --> pdb=" O   GLY J 702 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'J' and resid 719 through 722
    Processing sheet with id=AC1, first strand: chain 'J' and resid 764 through 769
      removed outlier: 5.744A  pdb=" N   TYR J 765 " --> pdb=" O   PHE J 748 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   PHE J 748 " --> pdb=" O   TYR J 765 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'J' and resid 924 through 925
      removed outlier: 3.751A  pdb=" N   PHE J 916 " --> pdb=" O   PHE J 904 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ARG J 901 " --> pdb=" O   PHE Z 895 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   VAL Z 897 " --> pdb=" O   ARG J 901 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA J 903 " --> pdb=" O   VAL Z 897 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ASP Z 886 " --> pdb=" O   TRP Z 859 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   TRP Z 859 " --> pdb=" O   ASP Z 886 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'Z' and resid 622 through 629
      removed outlier: 6.054A  pdb=" N   HIS Z 623 " --> pdb=" O   ASP Z 642 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ASP Z 642 " --> pdb=" O   HIS Z 623 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'Z' and resid 665 through 673
      removed outlier: 5.731A  pdb=" N   LEU Z 667 " --> pdb=" O   VAL Z 658 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL Z 658 " --> pdb=" O   LEU Z 667 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   ASN Z 687 " --> pdb=" O   THR Z 659 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'Z' and resid 719 through 721
    Processing sheet with id=AC6, first strand: chain 'Z' and resid 764 through 769
      removed outlier: 5.664A  pdb=" N   TYR Z 765 " --> pdb=" O   PHE Z 748 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE Z 748 " --> pdb=" O   TYR Z 765 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER Z 791 " --> pdb=" O   ALA Z 799 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   ALA Z 799 " --> pdb=" O   SER Z 791 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'Z' and resid 938 through 939

    312 hydrogen bonds defined for protein.
    810 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: 3.40

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1745
        1.32 -     1.47: 2371
        1.47 -     1.62: 4891
        1.62 -     1.77: 0
        1.77 -     1.91: 27
  Bond restraints: 9034
  Sorted by residual:
  bond pdb=" C   VAL F 621 "
       pdb=" O   VAL F 621 "
    ideal  model  delta    sigma   weight residual
    1.236  1.309 -0.073 1.03e-02 9.43e+03 5.03e+01
  bond pdb=" C   PHE F 924 "
       pdb=" O   PHE F 924 "
    ideal  model  delta    sigma   weight residual
    1.235  1.322 -0.087 1.23e-02 6.61e+03 5.01e+01
  bond pdb=" C   ILE F 938 "
       pdb=" O   ILE F 938 "
    ideal  model  delta    sigma   weight residual
    1.233  1.304 -0.071 1.08e-02 8.57e+03 4.33e+01
  bond pdb=" C   LEU Z 667 "
       pdb=" O   LEU Z 667 "
    ideal  model  delta    sigma   weight residual
    1.234  1.312 -0.077 1.20e-02 6.94e+03 4.14e+01
  bond pdb=" C   ILE F 923 "
       pdb=" O   ILE F 923 "
    ideal  model  delta    sigma   weight residual
    1.235  1.302 -0.066 1.05e-02 9.07e+03 4.01e+01
  ... (remaining 9029 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 9990
        2.94 -     5.88: 2066
        5.88 -     8.82: 203
        8.82 -    11.76: 24
       11.76 -    14.70: 10
  Bond angle restraints: 12293
  Sorted by residual:
  angle pdb=" C   SER J 970 "
        pdb=" N   GLY J 971 "
        pdb=" CA  GLY J 971 "
      ideal   model   delta    sigma   weight residual
     121.61  129.44   -7.83 7.70e-01 1.69e+00 1.03e+02
  angle pdb=" C   PHE J 895 "
        pdb=" N   LEU J 896 "
        pdb=" CA  LEU J 896 "
      ideal   model   delta    sigma   weight residual
     123.07  108.53   14.54 1.46e+00 4.69e-01 9.92e+01
  angle pdb=" C   PHE Z 895 "
        pdb=" CA  PHE Z 895 "
        pdb=" CB  PHE Z 895 "
      ideal   model   delta    sigma   weight residual
     111.82   98.36   13.46 1.38e+00 5.25e-01 9.51e+01
  angle pdb=" CA  TYR J 771 "
        pdb=" C   TYR J 771 "
        pdb=" O   TYR J 771 "
      ideal   model   delta    sigma   weight residual
     121.11  109.99   11.12 1.17e+00 7.31e-01 9.03e+01
  angle pdb=" CA  ASN J 900 "
        pdb=" CB  ASN J 900 "
        pdb=" CG  ASN J 900 "
      ideal   model   delta    sigma   weight residual
     112.60  103.77    8.83 1.00e+00 1.00e+00 7.80e+01
  ... (remaining 12288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4353
       17.59 -    35.19: 767
       35.19 -    52.78: 175
       52.78 -    70.38: 43
       70.38 -    87.97: 15
  Dihedral angle restraints: 5353
    sinusoidal: 2055
      harmonic: 3298
  Sorted by residual:
  dihedral pdb=" CA  ALA F 713 "
           pdb=" C   ALA F 713 "
           pdb=" N   PRO F 714 "
           pdb=" CA  PRO F 714 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -116.58  -63.42     0      5.00e+00 4.00e-02 1.61e+02
  dihedral pdb=" CA  ASN Z 943 "
           pdb=" C   ASN Z 943 "
           pdb=" N   PRO Z 944 "
           pdb=" CA  PRO Z 944 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.30   59.70     0      5.00e+00 4.00e-02 1.43e+02
  dihedral pdb=" CA  ALA Z 878 "
           pdb=" C   ALA Z 878 "
           pdb=" N   GLY Z 879 "
           pdb=" CA  GLY Z 879 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.99  -42.01     0      5.00e+00 4.00e-02 7.06e+01
  ... (remaining 5350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 564
       0.064 -    0.127: 488
       0.127 -    0.190: 238
       0.190 -    0.254: 89
       0.254 -    0.317: 16
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CA  GLN Z 922 "
            pdb=" N   GLN Z 922 "
            pdb=" C   GLN Z 922 "
            pdb=" CB  GLN Z 922 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  ILE J 905 "
            pdb=" N   ILE J 905 "
            pdb=" C   ILE J 905 "
            pdb=" CB  ILE J 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CA  PHE Z 904 "
            pdb=" N   PHE Z 904 "
            pdb=" C   PHE Z 904 "
            pdb=" CB  PHE Z 904 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1392 not shown)

  Planarity restraints: 1594
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J 876 "    0.091 2.00e-02 2.50e+03   4.66e-02 4.34e+01
        pdb=" CG  TYR J 876 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR J 876 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR J 876 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 TYR J 876 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR J 876 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR J 876 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR J 876 "    0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR J 814 "   -0.028 2.00e-02 2.50e+03   4.01e-02 3.22e+01
        pdb=" CG  TYR J 814 "    0.088 2.00e-02 2.50e+03
        pdb=" CD1 TYR J 814 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR J 814 "   -0.045 2.00e-02 2.50e+03
        pdb=" CE1 TYR J 814 "   -0.044 2.00e-02 2.50e+03
        pdb=" CE2 TYR J 814 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR J 814 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR J 814 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F 929 "   -0.057 2.00e-02 2.50e+03   4.00e-02 2.80e+01
        pdb=" CG  PHE F 929 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE F 929 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 PHE F 929 "    0.052 2.00e-02 2.50e+03
        pdb=" CE1 PHE F 929 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE F 929 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE F 929 "   -0.056 2.00e-02 2.50e+03
  ... (remaining 1591 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.20: 17
        2.20 -     2.88: 2940
        2.88 -     3.55: 12999
        3.55 -     4.23: 20810
        4.23 -     4.90: 33700
  Nonbonded interactions: 70466
  Sorted by model distance:
  nonbonded pdb=" N   ASN J 900 "
            pdb=" OG  SER Z 893 "
     model   vdw
     1.529 3.120
  nonbonded pdb=" OG  SER Z 776 "
            pdb=" OD1 ASN Z 778 "
     model   vdw
     1.973 3.040
  nonbonded pdb=" O   TRP J 859 "
            pdb=" NZ  LYS J 891 "
     model   vdw
     1.988 3.120
  nonbonded pdb=" O   ALA Z 684 "
            pdb=" OH  TYR Z 688 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" OE1 GLU Z 721 "
            pdb=" OG1 THR Z 732 "
     model   vdw
     2.030 3.040
  ... (remaining 70461 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 'F'
  selection = chain 'J'
  selection = (chain 'Z' and resid 616 through 995)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.010
  Find NCS groups from input model:        0.360
  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:             0.000
  Load rotamer database and sin/cos tables:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
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      :  0.017   0.111   9034  Z= 1.137
  Angle     :  2.344  14.704  12293  Z= 1.597
  Chirality :  0.108   0.317   1395
  Planarity :  0.010   0.064   1594
  Dihedral  : 19.303  87.972   3231
  Min Nonbonded Distance : 1.529

Molprobity Statistics.
  All-atom Clashscore : 43.22
  Ramachandran Plot:
    Outliers :  3.34 %
    Allowed  : 14.07 %
    Favored  : 82.59 %
  Rotamer:
    Outliers : 14.39 %
    Allowed  : 25.05 %
    Favored  : 60.55 %
  Cbeta Deviations :  1.04 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.64 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.22), residues: 1137
  helix: -3.24 (0.45), residues: 60
  sheet: -1.60 (0.28), residues: 332
  loop : -3.03 (0.19), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.007   TRP F 772 
 HIS   0.014   0.004   HIS Z 734 
 PHE   0.065   0.011   PHE J 904 
 TYR   0.091   0.010   TYR J 876 
 ARG   0.011   0.001   ARG J 806 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 135
    poor density    : 78
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  679 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8557 (tmm-80)
REVERT: F  797 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7489 (mmtt)
REVERT: F  837 LEU cc_start: 0.4958 (OUTLIER) cc_final: 0.4594 (tm)
REVERT: F  839 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6284 (mp0)
REVERT: F  844 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8861 (ttt180)
REVERT: F  847 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7735 (tm-30)
REVERT: F  932 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8340 (ttp80)
REVERT: F  943 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7780 (t0)
REVERT: F  976 VAL cc_start: 0.8040 (t) cc_final: 0.7734 (p)
REVERT: J  764 ARG cc_start: 0.7536 (tpp80) cc_final: 0.6855 (ttt-90)
REVERT: J  772 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.3674 (m100)
REVERT: J  837 LEU cc_start: 0.8642 (mt) cc_final: 0.8141 (mt)
REVERT: J  917 VAL cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (t)
REVERT: J  923 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8577 (mp)
REVERT: J  932 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8064 (mtm-85)
REVERT: Z  771 TYR cc_start: 0.9275 (OUTLIER) cc_final: 0.8856 (p90)
REVERT: Z  812 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9219 (tm-30)
REVERT: Z  832 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6357 (mt)
REVERT: Z  884 MET cc_start: 0.8328 (ptm) cc_final: 0.8125 (ptm)
REVERT: Z  902 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8799 (mt)
  outliers start: 135
  outliers final: 75
  residues processed: 202
  average time/residue: 0.2167
  time to fit residues: 59.4142
Evaluate side-chains
  153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 64
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  623 HIS
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  679 ARG
Chi-restraints excluded: chain F residue  687 ASN
Chi-restraints excluded: chain F residue  723 THR
Chi-restraints excluded: chain F residue  732 THR
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  797 LYS
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  821 LYS
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  839 GLU
Chi-restraints excluded: chain F residue  844 ARG
Chi-restraints excluded: chain F residue  847 GLU
Chi-restraints excluded: chain F residue  849 SER
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  892 LEU
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  902 ILE
Chi-restraints excluded: chain F residue  913 THR
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  917 VAL
Chi-restraints excluded: chain F residue  921 ASN
Chi-restraints excluded: chain F residue  943 ASN
Chi-restraints excluded: chain F residue  955 LEU
Chi-restraints excluded: chain F residue  985 ASN
Chi-restraints excluded: chain F residue  987 THR
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  677 THR
Chi-restraints excluded: chain J residue  685 LEU
Chi-restraints excluded: chain J residue  687 ASN
Chi-restraints excluded: chain J residue  720 ILE
Chi-restraints excluded: chain J residue  721 GLU
Chi-restraints excluded: chain J residue  762 SER
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  773 ILE
Chi-restraints excluded: chain J residue  780 LYS
Chi-restraints excluded: chain J residue  822 ILE
Chi-restraints excluded: chain J residue  845 LEU
Chi-restraints excluded: chain J residue  880 ILE
Chi-restraints excluded: chain J residue  905 ILE
Chi-restraints excluded: chain J residue  917 VAL
Chi-restraints excluded: chain J residue  921 ASN
Chi-restraints excluded: chain J residue  923 ILE
Chi-restraints excluded: chain J residue  928 VAL
Chi-restraints excluded: chain J residue  940 SER
Chi-restraints excluded: chain J residue  949 LEU
Chi-restraints excluded: chain J residue  950 THR
Chi-restraints excluded: chain J residue  955 LEU
Chi-restraints excluded: chain J residue  961 ASP
Chi-restraints excluded: chain J residue  962 ILE
Chi-restraints excluded: chain J residue  973 LEU
Chi-restraints excluded: chain J residue  983 THR
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  632 SER
Chi-restraints excluded: chain Z residue  635 TYR
Chi-restraints excluded: chain Z residue  646 VAL
Chi-restraints excluded: chain Z residue  656 LEU
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  682 GLN
Chi-restraints excluded: chain Z residue  695 VAL
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  777 ILE
Chi-restraints excluded: chain Z residue  780 LYS
Chi-restraints excluded: chain Z residue  791 SER
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  812 GLU
Chi-restraints excluded: chain Z residue  832 LEU
Chi-restraints excluded: chain Z residue  867 ILE
Chi-restraints excluded: chain Z residue  877 VAL
Chi-restraints excluded: chain Z residue  880 ILE
Chi-restraints excluded: chain Z residue  897 VAL
Chi-restraints excluded: chain Z residue  902 ILE
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  916 PHE
Chi-restraints excluded: chain Z residue  921 ASN
Chi-restraints excluded: chain Z residue  929 PHE
Chi-restraints excluded: chain Z residue  931 LYS
Chi-restraints excluded: chain Z residue  933 LEU
Chi-restraints excluded: chain Z residue  945 PRO
Chi-restraints excluded: chain Z residue  958 LYS
Chi-restraints excluded: chain Z residue  961 ASP
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  982 CYS
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:   30.0000
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
F 728 GLN
J 981 ASN
Z 826 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.134241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.111355 restraints weight = 20820.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.113006 restraints weight = 12206.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.113937 restraints weight = 8685.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9034  Z= 0.241
  Angle     :  0.801   9.348  12293  Z= 0.414
  Chirality :  0.049   0.166   1395
  Planarity :  0.006   0.103   1594
  Dihedral  : 11.784  87.622   1401
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  8.09 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 29.21 %
    Favored  : 63.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.25 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.23), residues: 1137
  helix: -1.31 (0.58), residues: 65
  sheet: -0.85 (0.25), residues: 413
  loop : -2.55 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP Z 698 
 HIS   0.004   0.001   HIS J 875 
 PHE   0.040   0.002   PHE Z 916 
 TYR   0.015   0.002   TYR F 814 
 ARG   0.008   0.001   ARG F 901 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 87
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  900 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6125 (t0)
REVERT: F  992 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7559 (mptt)
REVERT: J  634 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6659 (tp30)
REVERT: J  666 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7439 (tmt170)
REVERT: J  764 ARG cc_start: 0.7249 (tpp80) cc_final: 0.6453 (ttt-90)
REVERT: J  772 TRP cc_start: 0.4305 (OUTLIER) cc_final: 0.2069 (m100)
REVERT: J  814 TYR cc_start: 0.5969 (m-80) cc_final: 0.5121 (m-80)
REVERT: J  837 LEU cc_start: 0.8300 (mt) cc_final: 0.7964 (mt)
REVERT: Z  672 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.2550 (ptt-90)
REVERT: Z  698 TRP cc_start: 0.7298 (m-90) cc_final: 0.7022 (m-90)
REVERT: Z  771 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7599 (p90)
  outliers start: 65
  outliers final: 33
  residues processed: 139
  average time/residue: 0.2355
  time to fit residues: 44.9165
Evaluate side-chains
  107 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 67
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  722 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  804 VAL
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  913 THR
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  917 VAL
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  720 ILE
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  787 PHE
Chi-restraints excluded: chain J residue  880 ILE
Chi-restraints excluded: chain J residue  921 ASN
Chi-restraints excluded: chain J residue  949 LEU
Chi-restraints excluded: chain J residue  962 ILE
Chi-restraints excluded: chain J residue  973 LEU
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  695 VAL
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  790 ARG
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  827 LEU
Chi-restraints excluded: chain Z residue  867 ILE
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  916 PHE
Chi-restraints excluded: chain Z residue  931 LYS
Chi-restraints excluded: chain Z residue  961 ASP
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 74 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 16 optimal weight:   20.0000
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 6 optimal weight:   10.0000
   chunk 53 optimal weight:    7.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 981 ASN
Z 826 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.128104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.106864 restraints weight = 21752.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.106792 restraints weight = 13001.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.108325 restraints weight = 10333.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.134   9034  Z= 0.547
  Angle     :  0.903  14.616  12293  Z= 0.460
  Chirality :  0.051   0.190   1395
  Planarity :  0.007   0.091   1594
  Dihedral  :  9.783  86.101   1279
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 18.67
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 13.54 %
    Favored  : 86.10 %
  Rotamer:
    Outliers :  9.28 %
    Allowed  : 30.28 %
    Favored  : 60.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.24), residues: 1137
  helix: -1.04 (0.66), residues: 65
  sheet: -0.99 (0.25), residues: 430
  loop : -2.70 (0.22), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP F 772 
 HIS   0.006   0.002   HIS Z 734 
 PHE   0.041   0.003   PHE Z 916 
 TYR   0.022   0.003   TYR Z 785 
 ARG   0.006   0.001   ARG F 844 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 61
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  845 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7811 (tt)
REVERT: F  900 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6289 (t0)
REVERT: F  992 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7561 (mptt)
REVERT: J  764 ARG cc_start: 0.7377 (tpp80) cc_final: 0.7169 (tpp80)
REVERT: J  772 TRP cc_start: 0.4706 (OUTLIER) cc_final: 0.2329 (m100)
REVERT: J  814 TYR cc_start: 0.6325 (m-80) cc_final: 0.5461 (m-80)
REVERT: Z  653 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8786 (tt)
REVERT: Z  672 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.3952 (ptt180)
REVERT: Z  698 TRP cc_start: 0.7224 (m-90) cc_final: 0.6860 (m-90)
REVERT: Z  991 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7202 (mp0)
  outliers start: 87
  outliers final: 53
  residues processed: 134
  average time/residue: 0.2145
  time to fit residues: 40.1751
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 57
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  653 LEU
Chi-restraints excluded: chain F residue  732 THR
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  742 VAL
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  786 TYR
Chi-restraints excluded: chain F residue  801 VAL
Chi-restraints excluded: chain F residue  804 VAL
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  913 THR
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  917 VAL
Chi-restraints excluded: chain F residue  939 THR
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  761 THR
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  787 PHE
Chi-restraints excluded: chain J residue  887 THR
Chi-restraints excluded: chain J residue  921 ASN
Chi-restraints excluded: chain J residue  949 LEU
Chi-restraints excluded: chain J residue  950 THR
Chi-restraints excluded: chain J residue  962 ILE
Chi-restraints excluded: chain J residue  973 LEU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  629 THR
Chi-restraints excluded: chain Z residue  646 VAL
Chi-restraints excluded: chain Z residue  653 LEU
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  677 THR
Chi-restraints excluded: chain Z residue  695 VAL
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  790 ARG
Chi-restraints excluded: chain Z residue  791 SER
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  827 LEU
Chi-restraints excluded: chain Z residue  867 ILE
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  921 ASN
Chi-restraints excluded: chain Z residue  931 LYS
Chi-restraints excluded: chain Z residue  939 THR
Chi-restraints excluded: chain Z residue  961 ASP
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 76 optimal weight:    0.3980
   chunk 107 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.134421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.111945 restraints weight = 20912.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.114344 restraints weight = 12036.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.115211 restraints weight = 8161.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9034  Z= 0.221
  Angle     :  0.703   9.789  12293  Z= 0.360
  Chirality :  0.046   0.217   1395
  Planarity :  0.005   0.082   1594
  Dihedral  :  8.293  51.447   1270
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.95 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 31.13 %
    Favored  : 62.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.24), residues: 1137
  helix: -0.33 (0.68), residues: 65
  sheet: -0.75 (0.25), residues: 440
  loop : -2.53 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP J 852 
 HIS   0.003   0.001   HIS F 734 
 PHE   0.030   0.002   PHE Z 916 
 TYR   0.011   0.001   TYR Z 785 
 ARG   0.003   0.000   ARG J 806 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 69
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8068 (pp) cc_final: 0.7722 (mt)
REVERT: F  900 ASN cc_start: 0.6836 (OUTLIER) cc_final: 0.6090 (t0)
REVERT: F  984 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7551 (mp)
REVERT: F  992 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7543 (mptt)
REVERT: J  634 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6406 (tp30)
REVERT: J  666 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7492 (tmt170)
REVERT: J  764 ARG cc_start: 0.7202 (tpp80) cc_final: 0.6954 (tpp80)
REVERT: J  772 TRP cc_start: 0.4146 (OUTLIER) cc_final: 0.1896 (m100)
REVERT: J  814 TYR cc_start: 0.5990 (m-80) cc_final: 0.5419 (m-80)
REVERT: Z  672 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.3063 (ptt-90)
REVERT: Z  698 TRP cc_start: 0.7248 (m-90) cc_final: 0.6920 (m-90)
REVERT: Z  743 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6386 (tm-30)
  outliers start: 59
  outliers final: 27
  residues processed: 119
  average time/residue: 0.2355
  time to fit residues: 37.8797
Evaluate side-chains
  97 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  653 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  913 THR
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  917 VAL
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  695 VAL
Chi-restraints excluded: chain Z residue  723 THR
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  790 ARG
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  867 ILE
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 11 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 100 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 83 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 687 ASN
** Z 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.134565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.112192 restraints weight = 21081.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.114667 restraints weight = 12047.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.115494 restraints weight = 7929.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9034  Z= 0.226
  Angle     :  0.673   9.039  12293  Z= 0.344
  Chirality :  0.046   0.166   1395
  Planarity :  0.005   0.078   1594
  Dihedral  :  7.198  52.066   1253
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  9.15 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 31.02 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.24), residues: 1137
  helix: -0.11 (0.69), residues: 65
  sheet: -0.69 (0.25), residues: 450
  loop : -2.43 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP J 852 
 HIS   0.004   0.001   HIS Z 826 
 PHE   0.028   0.002   PHE Z 916 
 TYR   0.009   0.001   TYR Z 876 
 ARG   0.002   0.000   ARG J 790 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 75
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8085 (pp) cc_final: 0.7736 (mt)
REVERT: F  900 ASN cc_start: 0.6887 (OUTLIER) cc_final: 0.6083 (t0)
REVERT: F  984 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7423 (mp)
REVERT: F  992 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7506 (mptt)
REVERT: J  634 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6308 (tp30)
REVERT: J  662 ASP cc_start: 0.7539 (p0) cc_final: 0.6081 (m-30)
REVERT: J  666 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7353 (tmt170)
REVERT: J  764 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6937 (tpp80)
REVERT: J  772 TRP cc_start: 0.4115 (OUTLIER) cc_final: 0.1735 (m100)
REVERT: J  814 TYR cc_start: 0.5980 (m-80) cc_final: 0.5377 (m-80)
REVERT: Z  672 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.3149 (ptt-90)
REVERT: Z  710 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7227 (ttm110)
REVERT: Z  743 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6360 (tm-30)
REVERT: Z  991 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7193 (mp0)
  outliers start: 58
  outliers final: 34
  residues processed: 125
  average time/residue: 0.2139
  time to fit residues: 37.0807
Evaluate side-chains
  105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 62
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  653 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  801 VAL
Chi-restraints excluded: chain F residue  804 VAL
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  913 THR
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  887 THR
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  695 VAL
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  790 ARG
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  867 ILE
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  975 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 106 optimal weight:    3.9990
   chunk 59 optimal weight:    7.9990
   chunk 102 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 687 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.136960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.115069 restraints weight = 20860.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.117169 restraints weight = 11990.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.118160 restraints weight = 8121.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9034  Z= 0.187
  Angle     :  0.656   9.742  12293  Z= 0.333
  Chirality :  0.045   0.186   1395
  Planarity :  0.005   0.073   1594
  Dihedral  :  6.858  52.918   1252
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  6.42 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 32.20 %
    Favored  : 62.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.24), residues: 1137
  helix:  0.01 (0.70), residues: 65
  sheet: -0.47 (0.25), residues: 442
  loop : -2.36 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP Z 698 
 HIS   0.003   0.001   HIS Z 734 
 PHE   0.027   0.002   PHE Z 709 
 TYR   0.015   0.001   TYR F 814 
 ARG   0.002   0.000   ARG J 901 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 78
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8009 (pp) cc_final: 0.7620 (mt)
REVERT: F  815 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7853 (mp)
REVERT: F  845 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7830 (tt)
REVERT: F  900 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.5888 (t0)
REVERT: F  984 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7570 (mp)
REVERT: F  992 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7389 (mptt)
REVERT: J  634 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6145 (tp30)
REVERT: J  662 ASP cc_start: 0.7439 (p0) cc_final: 0.6180 (m-30)
REVERT: J  772 TRP cc_start: 0.3989 (OUTLIER) cc_final: 0.1316 (m100)
REVERT: J  814 TYR cc_start: 0.5894 (m-80) cc_final: 0.5385 (m-80)
REVERT: Z  672 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.3102 (ptt-90)
REVERT: Z  698 TRP cc_start: 0.7361 (m-90) cc_final: 0.6968 (m-90)
REVERT: Z  743 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6351 (tm-30)
REVERT: Z  771 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7778 (p90)
  outliers start: 50
  outliers final: 29
  residues processed: 120
  average time/residue: 0.2128
  time to fit residues: 35.9577
Evaluate side-chains
  108 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 69
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  892 LEU
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  887 THR
Chi-restraints excluded: chain J residue  973 LEU
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  687 ASN
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  773 ILE
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  882 LEU
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  975 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 37 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 87 optimal weight:    0.1980
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 778 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.133199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.111004 restraints weight = 21360.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.112897 restraints weight = 12267.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.114208 restraints weight = 8020.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   9034  Z= 0.329
  Angle     :  0.712   9.896  12293  Z= 0.362
  Chirality :  0.046   0.165   1395
  Planarity :  0.006   0.074   1594
  Dihedral  :  6.922  52.795   1246
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 10.38 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 31.45 %
    Favored  : 62.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.19 (0.24), residues: 1137
  helix:  0.01 (0.71), residues: 65
  sheet: -0.50 (0.25), residues: 435
  loop : -2.42 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP Z 698 
 HIS   0.004   0.001   HIS F 734 
 PHE   0.032   0.002   PHE Z 916 
 TYR   0.021   0.002   TYR Z 688 
 ARG   0.012   0.000   ARG Z 710 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 65
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8118 (pp) cc_final: 0.7722 (mt)
REVERT: F  815 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7887 (mp)
REVERT: F  845 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7840 (tt)
REVERT: F  900 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6007 (t0)
REVERT: F  984 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7437 (mp)
REVERT: F  992 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7532 (mptt)
REVERT: J  634 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6249 (tp30)
REVERT: J  772 TRP cc_start: 0.4067 (OUTLIER) cc_final: 0.1617 (m100)
REVERT: J  814 TYR cc_start: 0.6098 (m-80) cc_final: 0.5432 (m-80)
REVERT: Z  653 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (tt)
REVERT: Z  672 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.3385 (ptt-90)
REVERT: Z  698 TRP cc_start: 0.7388 (m-90) cc_final: 0.6926 (m-90)
REVERT: Z  711 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6443 (pp)
REVERT: Z  991 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7188 (mp0)
  outliers start: 58
  outliers final: 38
  residues processed: 114
  average time/residue: 0.2618
  time to fit residues: 41.2222
Evaluate side-chains
  111 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 62
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  653 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  801 VAL
Chi-restraints excluded: chain F residue  804 VAL
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  761 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  777 ILE
Chi-restraints excluded: chain J residue  950 THR
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  653 LEU
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  711 ILE
Chi-restraints excluded: chain Z residue  723 THR
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  773 ILE
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  882 LEU
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  909 ASN
Chi-restraints excluded: chain Z residue  975 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 107 optimal weight:    0.7980
   chunk 81 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 106 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 99 optimal weight:    0.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.134303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.112350 restraints weight = 21472.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.113605 restraints weight = 12504.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.114697 restraints weight = 8736.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   9034  Z= 0.265
  Angle     :  0.691   9.065  12293  Z= 0.351
  Chirality :  0.045   0.170   1395
  Planarity :  0.005   0.072   1594
  Dihedral  :  6.889  52.360   1246
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  8.88 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 31.77 %
    Favored  : 62.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.24), residues: 1137
  helix: -0.02 (0.70), residues: 65
  sheet: -0.46 (0.25), residues: 441
  loop : -2.40 (0.23), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP J 852 
 HIS   0.004   0.001   HIS Z 826 
 PHE   0.026   0.002   PHE Z 916 
 TYR   0.011   0.001   TYR F 814 
 ARG   0.013   0.000   ARG Z 710 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 67
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8077 (pp) cc_final: 0.7692 (mt)
REVERT: F  815 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7749 (mp)
REVERT: F  845 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7845 (tt)
REVERT: F  900 ASN cc_start: 0.6703 (OUTLIER) cc_final: 0.5761 (t0)
REVERT: F  984 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7423 (mp)
REVERT: F  992 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7493 (mptt)
REVERT: J  634 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6210 (tp30)
REVERT: J  662 ASP cc_start: 0.7639 (p0) cc_final: 0.6117 (m-30)
REVERT: J  666 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7378 (tmt170)
REVERT: J  772 TRP cc_start: 0.4181 (OUTLIER) cc_final: 0.1647 (m100)
REVERT: J  814 TYR cc_start: 0.6057 (m-80) cc_final: 0.5407 (m-80)
REVERT: Z  653 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8531 (tt)
REVERT: Z  672 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.3331 (ptt-90)
REVERT: Z  711 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6366 (pp)
REVERT: Z  743 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6391 (tm-30)
REVERT: Z  991 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7166 (mp0)
  outliers start: 55
  outliers final: 37
  residues processed: 114
  average time/residue: 0.2178
  time to fit residues: 34.7003
Evaluate side-chains
  115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 65
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  631 ASP
Chi-restraints excluded: chain F residue  653 LEU
Chi-restraints excluded: chain F residue  656 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  865 VAL
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  761 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  777 ILE
Chi-restraints excluded: chain J residue  852 TRP
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  653 LEU
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  711 ILE
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  773 ILE
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  882 LEU
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  909 ASN
Chi-restraints excluded: chain Z residue  975 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 112 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0270
   chunk 72 optimal weight:    0.8980
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.137890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.115904 restraints weight = 21098.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.118236 restraints weight = 11810.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.119170 restraints weight = 7923.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.3740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9034  Z= 0.182
  Angle     :  0.657   7.450  12293  Z= 0.335
  Chirality :  0.045   0.169   1395
  Planarity :  0.005   0.067   1594
  Dihedral  :  6.581  54.687   1246
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  7.30 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 32.41 %
    Favored  : 62.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.25), residues: 1137
  helix:  0.11 (0.72), residues: 65
  sheet: -0.42 (0.25), residues: 455
  loop : -2.24 (0.24), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP J 852 
 HIS   0.003   0.001   HIS F 734 
 PHE   0.020   0.001   PHE Z 709 
 TYR   0.009   0.001   TYR F 814 
 ARG   0.014   0.000   ARG Z 710 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 83
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8001 (pp) cc_final: 0.7615 (mt)
REVERT: F  845 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7913 (tt)
REVERT: F  900 ASN cc_start: 0.6491 (OUTLIER) cc_final: 0.5630 (t0)
REVERT: F  984 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7376 (mp)
REVERT: F  992 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7462 (mptt)
REVERT: J  634 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6042 (tp30)
REVERT: J  662 ASP cc_start: 0.7566 (p0) cc_final: 0.6060 (m-30)
REVERT: J  666 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7329 (tmt170)
REVERT: J  772 TRP cc_start: 0.4079 (OUTLIER) cc_final: 0.1106 (m100)
REVERT: J  814 TYR cc_start: 0.5873 (m-80) cc_final: 0.5355 (m-80)
REVERT: J  824 GLU cc_start: 0.7943 (pp20) cc_final: 0.7636 (pp20)
REVERT: Z  672 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.3242 (ptt-90)
REVERT: Z  698 TRP cc_start: 0.6919 (m-90) cc_final: 0.6549 (m-90)
REVERT: Z  711 ILE cc_start: 0.6286 (OUTLIER) cc_final: 0.6058 (pp)
REVERT: Z  743 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6321 (tm-30)
REVERT: Z  771 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7884 (p90)
REVERT: Z  991 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: Z  994 VAL cc_start: 0.4541 (OUTLIER) cc_final: 0.4284 (p)
  outliers start: 48
  outliers final: 28
  residues processed: 122
  average time/residue: 0.2398
  time to fit residues: 42.7163
Evaluate side-chains
  114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 73
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  656 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  761 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  852 TRP
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  711 ILE
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  909 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0970
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:   20.0000
   chunk 17 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0970
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
** F 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.136599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.114607 restraints weight = 21206.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.117060 restraints weight = 12057.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.117921 restraints weight = 8006.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9034  Z= 0.225
  Angle     :  0.673   7.161  12293  Z= 0.342
  Chirality :  0.045   0.162   1395
  Planarity :  0.005   0.065   1594
  Dihedral  :  6.559  55.059   1246
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  8.00 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 33.05 %
    Favored  : 61.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.25), residues: 1137
  helix:  0.17 (0.72), residues: 65
  sheet: -0.47 (0.25), residues: 447
  loop : -2.22 (0.23), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP J 852 
 HIS   0.003   0.001   HIS F 734 
 PHE   0.024   0.002   PHE J 817 
 TYR   0.016   0.001   TYR J 688 
 ARG   0.016   0.000   ARG Z 710 

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 73
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  773 ILE cc_start: 0.8021 (pp) cc_final: 0.7635 (mt)
REVERT: F  815 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: F  845 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7879 (tt)
REVERT: F  900 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.5941 (t0)
REVERT: F  984 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7448 (mp)
REVERT: F  992 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7496 (mptt)
REVERT: J  634 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6061 (tp30)
REVERT: J  662 ASP cc_start: 0.7604 (p0) cc_final: 0.6102 (m-30)
REVERT: J  666 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7438 (tmt170)
REVERT: J  688 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6860 (m-10)
REVERT: J  710 ARG cc_start: 0.8075 (ptp-170) cc_final: 0.7824 (ptm160)
REVERT: J  772 TRP cc_start: 0.4256 (OUTLIER) cc_final: 0.1201 (m100)
REVERT: J  814 TYR cc_start: 0.5931 (m-80) cc_final: 0.5357 (m-80)
REVERT: J  824 GLU cc_start: 0.7954 (pp20) cc_final: 0.7669 (pp20)
REVERT: Z  653 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: Z  672 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.3474 (ptt-90)
REVERT: Z  711 ILE cc_start: 0.6343 (OUTLIER) cc_final: 0.6104 (pp)
REVERT: Z  743 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6356 (tm-30)
REVERT: Z  771 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7877 (p90)
REVERT: Z  991 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7133 (mp0)
REVERT: Z  994 VAL cc_start: 0.4660 (OUTLIER) cc_final: 0.4410 (p)
  outliers start: 48
  outliers final: 31
  residues processed: 113
  average time/residue: 0.2556
  time to fit residues: 39.7343
Evaluate side-chains
  117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 70
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  624 LEU
Chi-restraints excluded: chain F residue  656 LEU
Chi-restraints excluded: chain F residue  734 HIS
Chi-restraints excluded: chain F residue  770 LEU
Chi-restraints excluded: chain F residue  804 VAL
Chi-restraints excluded: chain F residue  815 LEU
Chi-restraints excluded: chain F residue  822 ILE
Chi-restraints excluded: chain F residue  836 GLU
Chi-restraints excluded: chain F residue  837 LEU
Chi-restraints excluded: chain F residue  838 THR
Chi-restraints excluded: chain F residue  845 LEU
Chi-restraints excluded: chain F residue  893 SER
Chi-restraints excluded: chain F residue  900 ASN
Chi-restraints excluded: chain F residue  915 MET
Chi-restraints excluded: chain F residue  954 LYS
Chi-restraints excluded: chain F residue  984 ILE
Chi-restraints excluded: chain F residue  992 LYS
Chi-restraints excluded: chain J residue  634 GLU
Chi-restraints excluded: chain J residue  654 LEU
Chi-restraints excluded: chain J residue  666 ARG
Chi-restraints excluded: chain J residue  688 TYR
Chi-restraints excluded: chain J residue  691 THR
Chi-restraints excluded: chain J residue  761 THR
Chi-restraints excluded: chain J residue  766 LEU
Chi-restraints excluded: chain J residue  772 TRP
Chi-restraints excluded: chain J residue  852 TRP
Chi-restraints excluded: chain J residue  980 GLU
Chi-restraints excluded: chain J residue  994 VAL
Chi-restraints excluded: chain Z residue  621 VAL
Chi-restraints excluded: chain Z residue  628 VAL
Chi-restraints excluded: chain Z residue  653 LEU
Chi-restraints excluded: chain Z residue  661 ASP
Chi-restraints excluded: chain Z residue  672 ARG
Chi-restraints excluded: chain Z residue  711 ILE
Chi-restraints excluded: chain Z residue  743 GLN
Chi-restraints excluded: chain Z residue  768 THR
Chi-restraints excluded: chain Z residue  771 TYR
Chi-restraints excluded: chain Z residue  773 ILE
Chi-restraints excluded: chain Z residue  792 VAL
Chi-restraints excluded: chain Z residue  795 VAL
Chi-restraints excluded: chain Z residue  823 THR
Chi-restraints excluded: chain Z residue  882 LEU
Chi-restraints excluded: chain Z residue  904 PHE
Chi-restraints excluded: chain Z residue  909 ASN
Chi-restraints excluded: chain Z residue  976 VAL
Chi-restraints excluded: chain Z residue  991 GLU
Chi-restraints excluded: chain Z residue  994 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1956 > 50:
  distance: 5 - 9:  15.957
  distance: 9 - 10:  26.450
  distance: 10 - 11:  23.137
  distance: 10 - 13:  25.016
  distance: 11 - 12:  35.603
  distance: 11 - 17:  20.170
  distance: 13 - 14:  15.147
  distance: 13 - 15:  19.475
  distance: 14 - 16:  29.229
  distance: 17 - 18:  27.291
  distance: 18 - 19:  16.208
  distance: 18 - 21:  17.826
  distance: 19 - 20:  33.839
  distance: 19 - 25:  17.885
  distance: 21 - 22:  31.737
  distance: 22 - 23:  32.729
  distance: 22 - 24:  24.598
  distance: 25 - 26:  17.847
  distance: 25 - 31:  16.943
  distance: 26 - 27:  18.967
  distance: 26 - 29:   9.006
  distance: 27 - 28:   9.728
  distance: 27 - 32:  14.503
  distance: 29 - 30:  19.334
  distance: 30 - 31:  22.259
  distance: 32 - 33:  12.321
  distance: 33 - 34:  14.207
  distance: 33 - 36:  14.107
  distance: 34 - 35:   7.268
  distance: 34 - 37:  13.946
  distance: 37 - 38:  11.482
  distance: 38 - 39:  37.356
  distance: 38 - 41:  12.276
  distance: 39 - 40:   7.972
  distance: 39 - 45:  26.267
  distance: 41 - 42:   9.542
  distance: 42 - 43:  15.881
  distance: 42 - 44:  14.927
  distance: 45 - 46:  33.064
  distance: 46 - 47:   8.147
  distance: 47 - 48:   4.500
  distance: 47 - 49:  10.021
  distance: 49 - 50:  12.902
  distance: 50 - 51:  27.775
  distance: 50 - 53:  16.117
  distance: 51 - 52:  20.041
  distance: 51 - 57:   5.754
  distance: 53 - 54:  21.457
  distance: 54 - 55:  26.920
  distance: 54 - 56:  19.051
  distance: 57 - 58:  10.380
  distance: 58 - 59:   8.492
  distance: 58 - 61:  13.041
  distance: 59 - 60:  16.528
  distance: 59 - 66:   4.075
  distance: 61 - 62:  24.708
  distance: 62 - 63:  12.798
  distance: 63 - 64:  29.011
  distance: 63 - 65:   9.843
  distance: 66 - 67:  13.993
  distance: 67 - 68:  33.775
  distance: 67 - 70:  27.116
  distance: 68 - 69:  20.655
  distance: 68 - 73:  30.527
  distance: 70 - 71:   7.105
  distance: 70 - 72:  19.685
  distance: 73 - 74:  13.057
  distance: 73 - 79:  17.216
  distance: 74 - 75:  15.322
  distance: 74 - 77:  17.645
  distance: 75 - 76:   3.063
  distance: 75 - 80:  23.512
  distance: 77 - 78:  15.117
  distance: 78 - 79:  27.490