Starting phenix.real_space_refine
on Fri Aug 22 21:22:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dya_27779/08_2025/8dya_27779.map"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.082
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      36      5.16       5
     C    5034      2.51       5
     N    1368      2.21       5
     O    1458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7896
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 2548
          Classifications: {'peptide': 388}
          Incomplete info: {'truncation_to_alanine': 159}
          Link IDs: {'PTRANS': 20, 'TRANS': 367}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 468
          Unresolved non-hydrogen angles: 592
          Unresolved non-hydrogen dihedrals: 355
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 9, 'GLN:plan1': 16, 'TYR:plan': 1, 'PHE:plan': 3, 'ARG:plan': 6, 'ASP:plan': 12, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 227
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.06, per 1000 atoms: 0.26
  Number of scatterers: 7896
  At special positions: 0
  Unit cell: (87, 94, 138, 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      36     16.00
     O    1458      8.00
     N    1368      7.00
     C    5034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 707 " - pdb=" SG  CYS B 883 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 883 " - pdb=" SG  CYS C 707 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.15
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 707 " - pdb=" SG  CYS C 883 " distance=2.00
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.15
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.16
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.02

  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
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 801 "
      " NAG A1302 " - " ASN A1134 "
      " NAG A1303 " - " ASN A1098 "
      " NAG A1304 " - " ASN A 709 "
      " NAG A1305 " - " ASN A1074 "
      " NAG A1306 " - " ASN A 717 "
      " NAG B1301 " - " ASN B 801 "
      " NAG B1302 " - " ASN B1134 "
      " NAG B1303 " - " ASN B1098 "
      " NAG B1304 " - " ASN B 709 "
      " NAG B1305 " - " ASN B1074 "
      " NAG B1306 " - " ASN B 717 "
      " NAG C1301 " - " ASN C 801 "
      " NAG C1302 " - " ASN C1134 "
      " NAG C1303 " - " ASN C1098 "
      " NAG C1304 " - " ASN C 709 "
      " NAG C1305 " - " ASN C1074 "
      " NAG C1306 " - " ASN C 717 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 420.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2196

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 12 sheets defined
      48.2% alpha, 14.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 752 through 783
    Processing helix  chain 'A' and resid 816 through 826
    Processing helix  chain 'A' and resid 866 through 884
    Processing helix  chain 'A' and resid 898 through 908
      removed outlier: 3.777A  pdb=" N   TYR A 904 " --> pdb=" O   MET A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 919
    Processing helix  chain 'A' and resid 919 through 941
      removed outlier: 3.622A  pdb=" N   SER A 939 " --> pdb=" O   GLN A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 965
      removed outlier: 3.603A  pdb=" N   ASN A 955 " --> pdb=" O   VAL A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 978 through 982
    Processing helix  chain 'A' and resid 985 through 1032
      removed outlier: 4.801A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1116 through 1118
      No H-bonds generated for 'chain 'A' and resid 1116 through 1118'
    Processing helix  chain 'A' and resid 1141 through 1149
    Processing helix  chain 'B' and resid 752 through 783
    Processing helix  chain 'B' and resid 816 through 826
    Processing helix  chain 'B' and resid 866 through 884
    Processing helix  chain 'B' and resid 898 through 908
      removed outlier: 3.776A  pdb=" N   TYR B 904 " --> pdb=" O   MET B 900 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 914 through 919
    Processing helix  chain 'B' and resid 919 through 941
      removed outlier: 3.622A  pdb=" N   SER B 939 " --> pdb=" O   GLN B 935 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 946 through 965
      removed outlier: 3.603A  pdb=" N   ASN B 955 " --> pdb=" O   VAL B 951 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 978 through 982
    Processing helix  chain 'B' and resid 985 through 1032
      removed outlier: 4.801A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1116 through 1118
      No H-bonds generated for 'chain 'B' and resid 1116 through 1118'
    Processing helix  chain 'B' and resid 1141 through 1149
    Processing helix  chain 'C' and resid 752 through 783
    Processing helix  chain 'C' and resid 816 through 826
    Processing helix  chain 'C' and resid 866 through 884
    Processing helix  chain 'C' and resid 898 through 908
      removed outlier: 3.777A  pdb=" N   TYR C 904 " --> pdb=" O   MET C 900 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 914 through 919
    Processing helix  chain 'C' and resid 919 through 941
      removed outlier: 3.621A  pdb=" N   SER C 939 " --> pdb=" O   GLN C 935 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 946 through 965
      removed outlier: 3.602A  pdb=" N   ASN C 955 " --> pdb=" O   VAL C 951 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 978 through 982
    Processing helix  chain 'C' and resid 985 through 1032
      removed outlier: 4.800A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1116 through 1118
      No H-bonds generated for 'chain 'C' and resid 1116 through 1118'
    Processing helix  chain 'C' and resid 1141 through 1149
    Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 715
      removed outlier: 4.524A  pdb=" N   PHE A1095 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 718 through 728
      removed outlier: 7.395A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1055 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   SER A1055 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL A1061 " --> pdb=" O   PRO A1053 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU A1063 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER A1051 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL A1065 " --> pdb=" O   LEU A1049 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 735
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1125
      removed outlier: 4.419A  pdb=" N   ALA A1087 " --> pdb=" O   SER A1123 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 711 through 715
      removed outlier: 4.524A  pdb=" N   PHE B1095 " --> pdb=" O   ALA B1078 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 718 through 728
      removed outlier: 7.395A  pdb=" N   GLY B1059 " --> pdb=" O   SER B1055 " (cutoff:3.500A)
      removed outlier: 5.840A  pdb=" N   SER B1055 " --> pdb=" O   GLY B1059 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B1061 " --> pdb=" O   PRO B1053 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU B1063 " --> pdb=" O   SER B1051 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   SER B1051 " --> pdb=" O   LEU B1063 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL B1065 " --> pdb=" O   LEU B1049 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 735
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1120 through 1125
      removed outlier: 4.419A  pdb=" N   ALA B1087 " --> pdb=" O   SER B1123 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 711 through 715
      removed outlier: 4.524A  pdb=" N   PHE C1095 " --> pdb=" O   ALA C1078 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 718 through 728
      removed outlier: 7.394A  pdb=" N   GLY C1059 " --> pdb=" O   SER C1055 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   SER C1055 " --> pdb=" O   GLY C1059 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL C1061 " --> pdb=" O   PRO C1053 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU C1063 " --> pdb=" O   SER C1051 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER C1051 " --> pdb=" O   LEU C1063 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL C1065 " --> pdb=" O   LEU C1049 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 734 through 735
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1120 through 1125
      removed outlier: 4.419A  pdb=" N   ALA C1087 " --> pdb=" O   SER C1123 " (cutoff:3.500A)

    516 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.23

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1828
        1.33 -     1.45: 1965
        1.45 -     1.58: 4202
        1.58 -     1.71: 6
        1.71 -     1.83: 54
  Bond restraints: 8055
  Sorted by residual:
  bond pdb=" CA  GLN A 804 "
       pdb=" C   GLN A 804 "
    ideal  model  delta    sigma   weight residual
    1.523  1.600 -0.077 1.34e-02 5.57e+03 3.29e+01
  bond pdb=" CA  GLN B 804 "
       pdb=" C   GLN B 804 "
    ideal  model  delta    sigma   weight residual
    1.523  1.600 -0.077 1.34e-02 5.57e+03 3.26e+01
  bond pdb=" CA  GLN C 804 "
       pdb=" C   GLN C 804 "
    ideal  model  delta    sigma   weight residual
    1.523  1.600 -0.077 1.34e-02 5.57e+03 3.26e+01
  bond pdb=" CA  PHE C 817 "
       pdb=" C   PHE C 817 "
    ideal  model  delta    sigma   weight residual
    1.523  1.588 -0.065 1.30e-02 5.92e+03 2.50e+01
  bond pdb=" CA  PHE B 817 "
       pdb=" C   PHE B 817 "
    ideal  model  delta    sigma   weight residual
    1.523  1.588 -0.065 1.30e-02 5.92e+03 2.50e+01
  ... (remaining 8050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.23: 10829
        4.23 -     8.46: 220
        8.46 -    12.69: 18
       12.69 -    16.92: 3
       16.92 -    21.15: 6
  Bond angle restraints: 11076
  Sorted by residual:
  angle pdb=" N   ALA C 956 "
        pdb=" CA  ALA C 956 "
        pdb=" C   ALA C 956 "
      ideal   model   delta    sigma   weight residual
     111.28  100.80   10.48 1.09e+00 8.42e-01 9.25e+01
  angle pdb=" CD1 LEU B 922 "
        pdb=" CG  LEU B 922 "
        pdb=" CD2 LEU B 922 "
      ideal   model   delta    sigma   weight residual
     110.80  131.95  -21.15 2.20e+00 2.07e-01 9.24e+01
  angle pdb=" CD1 LEU A 922 "
        pdb=" CG  LEU A 922 "
        pdb=" CD2 LEU A 922 "
      ideal   model   delta    sigma   weight residual
     110.80  131.92  -21.12 2.20e+00 2.07e-01 9.21e+01
  angle pdb=" N   ALA A 956 "
        pdb=" CA  ALA A 956 "
        pdb=" C   ALA A 956 "
      ideal   model   delta    sigma   weight residual
     111.28  100.82   10.46 1.09e+00 8.42e-01 9.20e+01
  angle pdb=" CD1 LEU C 922 "
        pdb=" CG  LEU C 922 "
        pdb=" CD2 LEU C 922 "
      ideal   model   delta    sigma   weight residual
     110.80  131.85  -21.05 2.20e+00 2.07e-01 9.16e+01
  ... (remaining 11071 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 4755
       17.80 -    35.59: 157
       35.59 -    53.38: 23
       53.38 -    71.18: 6
       71.18 -    88.97: 6
  Dihedral angle restraints: 4947
    sinusoidal: 1575
      harmonic: 3372
  Sorted by residual:
  dihedral pdb=" N   ILE B 805 "
           pdb=" C   ILE B 805 "
           pdb=" CA  ILE B 805 "
           pdb=" CB  ILE B 805 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  137.30  -13.90     0      2.50e+00 1.60e-01 3.09e+01
  dihedral pdb=" N   ILE A 805 "
           pdb=" C   ILE A 805 "
           pdb=" CA  ILE A 805 "
           pdb=" CB  ILE A 805 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  137.27  -13.87     0      2.50e+00 1.60e-01 3.08e+01
  dihedral pdb=" N   ILE C 805 "
           pdb=" C   ILE C 805 "
           pdb=" CA  ILE C 805 "
           pdb=" CB  ILE C 805 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  137.21  -13.81     0      2.50e+00 1.60e-01 3.05e+01
  ... (remaining 4944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.147: 1233
       0.147 -    0.294: 114
       0.294 -    0.440: 26
       0.440 -    0.587: 1
       0.587 -    0.734: 3
  Chirality restraints: 1377
  Sorted by residual:
  chirality pdb=" C1  NAG A1306 "
            pdb=" ND2 ASN A 717 "
            pdb=" C2  NAG A1306 "
            pdb=" O5  NAG A1306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.67   -0.73 2.00e-01 2.50e+01 1.35e+01
  chirality pdb=" C1  NAG C1306 "
            pdb=" ND2 ASN C 717 "
            pdb=" C2  NAG C1306 "
            pdb=" O5  NAG C1306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.67   -0.73 2.00e-01 2.50e+01 1.34e+01
  chirality pdb=" C1  NAG B1306 "
            pdb=" ND2 ASN B 717 "
            pdb=" C2  NAG B1306 "
            pdb=" O5  NAG B1306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.67   -0.73 2.00e-01 2.50e+01 1.34e+01
  ... (remaining 1374 not shown)

  Planarity restraints: 1482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 817 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.03e+00
        pdb=" C   PHE B 817 "    0.042 2.00e-02 2.50e+03
        pdb=" O   PHE B 817 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ILE B 818 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 817 "    0.012 2.00e-02 2.50e+03   2.45e-02 6.01e+00
        pdb=" C   PHE C 817 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   PHE C 817 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE C 818 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 817 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.96e+00
        pdb=" C   PHE A 817 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   PHE A 817 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A 818 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1479 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.01: 4257
        3.01 -     3.48: 7691
        3.48 -     3.95: 12087
        3.95 -     4.43: 13300
        4.43 -     4.90: 21267
  Nonbonded interactions: 58602
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 733 "
            pdb=" OD2 ASP C 775 "
     model   vdw
     2.532 3.120
  nonbonded pdb=" NZ  LYS B 733 "
            pdb=" OD2 ASP B 775 "
     model   vdw
     2.533 3.120
  nonbonded pdb=" NZ  LYS A 733 "
            pdb=" OD2 ASP A 775 "
     model   vdw
     2.533 3.120
  nonbonded pdb=" N   ASP C 775 "
            pdb=" N   LYS C 776 "
     model   vdw
     2.537 2.560
  nonbonded pdb=" N   ASP A 775 "
            pdb=" N   LYS A 776 "
     model   vdw
     2.537 2.560
  ... (remaining 58597 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.890
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.010
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
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      :  0.011   0.167   8082  Z= 0.637
  Angle     :  1.527  21.149  11148  Z= 1.010
  Chirality :  0.095   0.734   1377
  Planarity :  0.005   0.025   1464
  Dihedral  :  9.995  88.972   2724
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  3.88 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.56 %
    Favored  : 98.88 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.22), residues: 1134
  helix:  1.64 (0.20), residues: 501
  sheet:  1.32 (0.36), residues: 129
  loop : -1.13 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 905 
 TYR   0.013   0.003   TYR B1067 
 PHE   0.013   0.003   PHE C 906 
 TRP   0.010   0.004   TRP C 886 
 HIS   0.004   0.001   HIS B1083 

Details of bonding type rmsd
  covalent geometry    : bond        0.00993 ( 8055)
  covalent geometry    : angle       1.49273 (11076)
  SS BOND              : bond        0.07478 (    9)
  SS BOND              : angle       5.70683 (   18)
  hydrogen bonds       : bond        0.18793 (  516)
  hydrogen bonds       : angle       6.29650 ( 1512)
  link_NAG-ASN         : bond        0.08613 (   18)
  link_NAG-ASN         : angle       3.67174 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 157
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  801 ASN cc_start: 0.7346 (t0) cc_final: 0.6962 (t0)
REVERT: C 1027 THR cc_start: 0.7695 (m) cc_final: 0.7476 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 158
  average time/residue: 0.0870
  time to fit residues: 19.1415
Evaluate side-chains
  76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    0.0570
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
B1011 GLN
B1106 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.208075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.200278 restraints weight = 8981.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.171439 restraints weight = 14190.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.173546 restraints weight = 12102.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.174036 restraints weight = 9865.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.174081 restraints weight = 9202.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8082  Z= 0.144
  Angle     :  0.622  17.343  11148  Z= 0.310
  Chirality :  0.045   0.365   1377
  Planarity :  0.005   0.051   1464
  Dihedral  :  5.701  51.526   1569
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.20 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  8.38 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.24), residues: 1134
  helix:  3.01 (0.21), residues: 522
  sheet:  0.86 (0.38), residues: 144
  loop : -1.26 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 815 
 TYR   0.018   0.002   TYR C1067 
 PHE   0.014   0.002   PHE C 782 
 TRP   0.009   0.001   TRP A1102 
 HIS   0.005   0.001   HIS A1064 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8055)
  covalent geometry    : angle       0.56140 (11076)
  SS BOND              : bond        0.00347 (    9)
  SS BOND              : angle       1.25972 (   18)
  hydrogen bonds       : bond        0.04578 (  516)
  hydrogen bonds       : angle       4.40554 ( 1512)
  link_NAG-ASN         : bond        0.01175 (   18)
  link_NAG-ASN         : angle       3.85019 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  902 MET cc_start: 0.7144 (mmm) cc_final: 0.6411 (tpt)
REVERT: C 1027 THR cc_start: 0.7504 (m) cc_final: 0.7180 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0821
  time to fit residues: 10.3100
Evaluate side-chains
  77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B 928 ASN
B1119 ASN
C1119 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.132713 restraints weight = 9029.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134271 restraints weight = 8858.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136702 restraints weight = 6775.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137264 restraints weight = 4964.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137785 restraints weight = 4769.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080   8082  Z= 0.222
  Angle     :  0.706  17.195  11148  Z= 0.347
  Chirality :  0.047   0.267   1377
  Planarity :  0.005   0.054   1464
  Dihedral  :  5.371  37.066   1569
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.06 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 10.24 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.24), residues: 1134
  helix:  3.13 (0.21), residues: 522
  sheet:  0.19 (0.38), residues: 144
  loop : -1.33 (0.24), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 815 
 TYR   0.020   0.002   TYR C1067 
 PHE   0.028   0.002   PHE B 906 
 TRP   0.014   0.002   TRP A1102 
 HIS   0.005   0.001   HIS C1064 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 8055)
  covalent geometry    : angle       0.64420 (11076)
  SS BOND              : bond        0.00618 (    9)
  SS BOND              : angle       1.25098 (   18)
  hydrogen bonds       : bond        0.04540 (  516)
  hydrogen bonds       : angle       4.33123 ( 1512)
  link_NAG-ASN         : bond        0.00731 (   18)
  link_NAG-ASN         : angle       4.14795 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  794 ILE cc_start: 0.6050 (mt) cc_final: 0.5393 (tt)
REVERT: A 1023 ASN cc_start: 0.6595 (m-40) cc_final: 0.6353 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0834
  time to fit residues: 9.8228
Evaluate side-chains
  74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1040 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  865 LEU
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0060
   chunk 33 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0010
   chunk 74 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9980
   chunk 61 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0570
   overall best weight:    0.2720

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

Flipped N/Q/H residues before XYZ refinement:
C1023 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.181654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.133125 restraints weight = 9007.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136961 restraints weight = 6252.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139225 restraints weight = 5001.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.141146 restraints weight = 4361.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.141999 restraints weight = 3984.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8082  Z= 0.106
  Angle     :  0.544  15.774  11148  Z= 0.266
  Chirality :  0.042   0.213   1377
  Planarity :  0.004   0.029   1464
  Dihedral  :  4.521  37.275   1569
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.12 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.10 %
    Favored  : 84.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.24), residues: 1134
  helix:  3.38 (0.21), residues: 522
  sheet:  0.82 (0.45), residues: 108
  loop : -1.23 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 815 
 TYR   0.021   0.001   TYR C1067 
 PHE   0.012   0.001   PHE B 823 
 TRP   0.006   0.001   TRP B1102 
 HIS   0.003   0.001   HIS C1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 8055)
  covalent geometry    : angle       0.49698 (11076)
  SS BOND              : bond        0.00210 (    9)
  SS BOND              : angle       0.71617 (   18)
  hydrogen bonds       : bond        0.03719 (  516)
  hydrogen bonds       : angle       3.91820 ( 1512)
  link_NAG-ASN         : bond        0.00589 (   18)
  link_NAG-ASN         : angle       3.20628 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  733 LYS cc_start: 0.8096 (pttt) cc_final: 0.7774 (pttp)
REVERT: B  779 GLN cc_start: 0.7877 (mt0) cc_final: 0.7590 (mm-40)
REVERT: B  900 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7565 (mtm)
  outliers start: 19
  outliers final: 13
  residues processed: 82
  average time/residue: 0.0804
  time to fit residues: 9.6430
Evaluate side-chains
  81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  707 CYS
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue  900 MET
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  779 GLN
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0980
   chunk 102 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   chunk 14 optimal weight:    0.7980
   chunk 97 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A1088 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.177267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.129166 restraints weight = 9002.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.132960 restraints weight = 6311.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135480 restraints weight = 5028.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136869 restraints weight = 4357.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137408 restraints weight = 4007.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8082  Z= 0.135
  Angle     :  0.564  15.489  11148  Z= 0.275
  Chirality :  0.043   0.221   1377
  Planarity :  0.004   0.031   1464
  Dihedral  :  4.454  38.043   1569
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.44 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.22 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.24), residues: 1134
  helix:  3.32 (0.21), residues: 528
  sheet:  0.37 (0.44), residues: 114
  loop : -1.11 (0.24), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 815 
 TYR   0.020   0.002   TYR C1067 
 PHE   0.012   0.001   PHE C1121 
 TRP   0.006   0.001   TRP B1102 
 HIS   0.003   0.001   HIS C1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8055)
  covalent geometry    : angle       0.51845 (11076)
  SS BOND              : bond        0.00354 (    9)
  SS BOND              : angle       0.90029 (   18)
  hydrogen bonds       : bond        0.03708 (  516)
  hydrogen bonds       : angle       3.84777 ( 1512)
  link_NAG-ASN         : bond        0.00523 (   18)
  link_NAG-ASN         : angle       3.18652 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  779 GLN cc_start: 0.7824 (mt0) cc_final: 0.7539 (mm-40)
REVERT: C  779 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7746 (mm-40)
  outliers start: 19
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0844
  time to fit residues: 9.8079
Evaluate side-chains
  80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  722 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  779 GLN
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 10 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 804 GLN
C1088 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.131315 restraints weight = 9025.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.128200 restraints weight = 7096.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.131511 restraints weight = 6493.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.131999 restraints weight = 5059.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132157 restraints weight = 4808.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.5252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   8082  Z= 0.185
  Angle     :  0.628  14.503  11148  Z= 0.309
  Chirality :  0.046   0.242   1377
  Planarity :  0.004   0.032   1464
  Dihedral  :  5.185  41.348   1569
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.53 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 13.97 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.24), residues: 1134
  helix:  3.15 (0.21), residues: 528
  sheet: -0.42 (0.37), residues: 144
  loop : -1.32 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B1019 
 TYR   0.023   0.002   TYR C1067 
 PHE   0.015   0.002   PHE B 906 
 TRP   0.008   0.002   TRP B1102 
 HIS   0.003   0.001   HIS B1064 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8055)
  covalent geometry    : angle       0.58564 (11076)
  SS BOND              : bond        0.00515 (    9)
  SS BOND              : angle       1.17271 (   18)
  hydrogen bonds       : bond        0.03976 (  516)
  hydrogen bonds       : angle       4.06355 ( 1512)
  link_NAG-ASN         : bond        0.00497 (   18)
  link_NAG-ASN         : angle       3.25176 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  869 MET cc_start: 0.6356 (mmm) cc_final: 0.6055 (mtp)
REVERT: B  779 GLN cc_start: 0.7957 (mt0) cc_final: 0.7626 (mm-40)
REVERT: C  779 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7833 (mm-40)
  outliers start: 19
  outliers final: 15
  residues processed: 80
  average time/residue: 0.0929
  time to fit residues: 10.3250
Evaluate side-chains
  80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1040 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  779 GLN
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0170
   chunk 15 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 59 optimal weight:   20.0000
   chunk 54 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
A 804 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.180751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.143942 restraints weight = 8632.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.146806 restraints weight = 6380.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.148698 restraints weight = 5218.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149778 restraints weight = 4552.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149778 restraints weight = 4176.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8082  Z= 0.113
  Angle     :  0.538  13.660  11148  Z= 0.262
  Chirality :  0.043   0.211   1377
  Planarity :  0.003   0.029   1464
  Dihedral  :  4.688  39.160   1569
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.82 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.53 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.24), residues: 1134
  helix:  3.35 (0.21), residues: 528
  sheet:  0.04 (0.43), residues: 114
  loop : -1.20 (0.24), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C1019 
 TYR   0.021   0.001   TYR C1067 
 PHE   0.011   0.001   PHE C1121 
 TRP   0.005   0.001   TRP B 886 
 HIS   0.003   0.001   HIS C1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8055)
  covalent geometry    : angle       0.50014 (11076)
  SS BOND              : bond        0.00264 (    9)
  SS BOND              : angle       0.71321 (   18)
  hydrogen bonds       : bond        0.03562 (  516)
  hydrogen bonds       : angle       3.83496 ( 1512)
  link_NAG-ASN         : bond        0.00480 (   18)
  link_NAG-ASN         : angle       2.89603 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  869 MET cc_start: 0.6103 (mmm) cc_final: 0.5779 (mtp)
REVERT: B  779 GLN cc_start: 0.7861 (mt0) cc_final: 0.7536 (mm-40)
REVERT: C  779 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7827 (mm-40)
  outliers start: 18
  outliers final: 15
  residues processed: 79
  average time/residue: 0.0915
  time to fit residues: 10.0551
Evaluate side-chains
  76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  707 CYS
Chi-restraints excluded: chain C residue  779 GLN
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 22 optimal weight:   50.0000
   chunk 96 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0870
   chunk 100 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 97 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    1.3962

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

Flipped N/Q/H residues before XYZ refinement:
B1088 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.184798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 132)---------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151773 restraints weight = 8410.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149967 restraints weight = 12989.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149969 restraints weight = 11431.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149969 restraints weight = 11385.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149969 restraints weight = 11385.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.5603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077   8082  Z= 0.227
  Angle     :  0.670  13.668  11148  Z= 0.330
  Chirality :  0.048   0.244   1377
  Planarity :  0.004   0.033   1464
  Dihedral  :  5.403  42.023   1569
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.76 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.83 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.24), residues: 1134
  helix:  3.09 (0.22), residues: 528
  sheet: -0.78 (0.34), residues: 144
  loop : -1.41 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 815 
 TYR   0.024   0.002   TYR C1067 
 PHE   0.019   0.002   PHE A 906 
 TRP   0.007   0.002   TRP B1102 
 HIS   0.005   0.002   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 8055)
  covalent geometry    : angle       0.63231 (11076)
  SS BOND              : bond        0.00631 (    9)
  SS BOND              : angle       1.34527 (   18)
  hydrogen bonds       : bond        0.04113 (  516)
  hydrogen bonds       : angle       4.18220 ( 1512)
  link_NAG-ASN         : bond        0.00515 (   18)
  link_NAG-ASN         : angle       3.16374 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A  869 MET cc_start: 0.6084 (mmm) cc_final: 0.5789 (mtp)
REVERT: B  779 GLN cc_start: 0.7966 (mt0) cc_final: 0.7687 (mm-40)
  outliers start: 17
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0899
  time to fit residues: 9.6166
Evaluate side-chains
  78 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 110 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.188580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.180188 restraints weight = 8248.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.176354 restraints weight = 11715.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.175068 restraints weight = 18173.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173699 restraints weight = 19127.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.173931 restraints weight = 16609.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.5679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8082  Z= 0.145
  Angle     :  0.588  13.097  11148  Z= 0.286
  Chirality :  0.045   0.227   1377
  Planarity :  0.004   0.045   1464
  Dihedral  :  5.065  40.963   1569
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.53 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.39 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.24), residues: 1134
  helix:  3.14 (0.21), residues: 510
  sheet: -0.84 (0.35), residues: 144
  loop : -1.41 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 815 
 TYR   0.022   0.001   TYR C1067 
 PHE   0.020   0.001   PHE B 823 
 TRP   0.007   0.002   TRP C 886 
 HIS   0.003   0.001   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8055)
  covalent geometry    : angle       0.55129 (11076)
  SS BOND              : bond        0.00407 (    9)
  SS BOND              : angle       1.01207 (   18)
  hydrogen bonds       : bond        0.03747 (  516)
  hydrogen bonds       : angle       4.01134 ( 1512)
  link_NAG-ASN         : bond        0.00472 (   18)
  link_NAG-ASN         : angle       2.95883 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  869 MET cc_start: 0.5521 (mmm) cc_final: 0.5227 (mtp)
REVERT: B  869 MET cc_start: 0.5937 (mmm) cc_final: 0.5544 (mmm)
  outliers start: 16
  outliers final: 16
  residues processed: 73
  average time/residue: 0.0884
  time to fit residues: 9.2626
Evaluate side-chains
  75 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1040 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  722 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 27 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   chunk 33 optimal weight:    0.5980
   chunk 35 optimal weight:    0.4980
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.191769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.183670 restraints weight = 8235.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.180354 restraints weight = 11952.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161926 restraints weight = 17243.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.161420 restraints weight = 16228.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.161936 restraints weight = 13390.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8082  Z= 0.111
  Angle     :  0.543  12.448  11148  Z= 0.264
  Chirality :  0.043   0.208   1377
  Planarity :  0.003   0.031   1464
  Dihedral  :  4.603  38.990   1569
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.53 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.08 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.24), residues: 1134
  helix:  3.27 (0.21), residues: 510
  sheet: -0.16 (0.42), residues: 114
  loop : -1.29 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 815 
 TYR   0.019   0.001   TYR C1067 
 PHE   0.011   0.001   PHE C1121 
 TRP   0.006   0.001   TRP B 886 
 HIS   0.003   0.001   HIS C1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8055)
  covalent geometry    : angle       0.51021 (11076)
  SS BOND              : bond        0.00296 (    9)
  SS BOND              : angle       0.77064 (   18)
  hydrogen bonds       : bond        0.03517 (  516)
  hydrogen bonds       : angle       3.83316 ( 1512)
  link_NAG-ASN         : bond        0.00438 (   18)
  link_NAG-ASN         : angle       2.69473 (   54)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  869 MET cc_start: 0.5909 (mmm) cc_final: 0.5574 (mtp)
  outliers start: 18
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0855
  time to fit residues: 9.7240
Evaluate side-chains
  77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1033 VAL
Chi-restraints excluded: chain A residue 1040 VAL
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  821 LEU
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  870 ILE
Chi-restraints excluded: chain C residue  874 THR
Chi-restraints excluded: chain C residue  896 ILE
Chi-restraints excluded: chain C residue 1104 VAL
Chi-restraints excluded: chain C residue 1122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0020
   chunk 25 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0980
   chunk 55 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.192875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.184615 restraints weight = 8206.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.179836 restraints weight = 12792.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.162797 restraints weight = 18647.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161346 restraints weight = 16856.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161608 restraints weight = 15137.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.5852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8082  Z= 0.110
  Angle     :  0.543  11.979  11148  Z= 0.262
  Chirality :  0.043   0.207   1377
  Planarity :  0.003   0.032   1464
  Dihedral  :  4.437  37.434   1569
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.44 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.83 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.24), residues: 1134
  helix:  3.33 (0.21), residues: 510
  sheet: -0.04 (0.43), residues: 114
  loop : -1.20 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 815 
 TYR   0.019   0.001   TYR C1067 
 PHE   0.011   0.001   PHE C1121 
 TRP   0.006   0.001   TRP B 886 
 HIS   0.003   0.001   HIS C1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8055)
  covalent geometry    : angle       0.51216 (11076)
  SS BOND              : bond        0.00279 (    9)
  SS BOND              : angle       0.78021 (   18)
  hydrogen bonds       : bond        0.03428 (  516)
  hydrogen bonds       : angle       3.78013 ( 1512)
  link_NAG-ASN         : bond        0.00410 (   18)
  link_NAG-ASN         : angle       2.61395 (   54)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1616.35 seconds
wall clock time: 28 minutes 23.72 seconds (1703.72 seconds total)