Starting phenix.real_space_refine
on Thu Jul  2 09:04:49 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_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 {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dya_27779/07_2026/8dya_27779.cif"
  }
  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-dev-6108/lib/python3.11/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 chiralities: 6
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.91, per 1000 atoms: 0.24
  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: 0.63
  Conformation dependent library (CDL) restraints added in 429.7 milliseconds
  

  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: 0.22
  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: 1.21

  Time building geometry restraints manager: 0.84 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: 4407
       17.80 -    35.59: 127
       35.59 -    53.38: 23
       53.38 -    71.18: 6
       71.18 -    88.97: 6
  Dihedral angle restraints: 4569
    sinusoidal: 1197
      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 4566 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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.370
  Find NCS groups from input model:        0.050
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
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  : 10.235  88.972   2346
  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 are 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/Z
  covalent geometry    : bond        0.00993 /  0.59 ( 8055)
  covalent geometry    : angle       1.49273 /  1.00 (11076)
  SS BOND              : bond        0.07478 /  4.57 (    9)
  SS BOND              : angle       5.70683 /  3.53 (   18)
  hydrogen bonds       : bond        0.18793 / 12.73 (  516)
  hydrogen bonds       : angle       6.29650 /  4.62 ( 1512)
  link_NAG-ASN         : bond        0.08613 /  5.76 (   18)
  link_NAG-ASN         : angle       3.67174 /  2.69 (   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  : 0.269 
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: 0.0760
  time to fit residues: 16.8732
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  : 0.240 
-------------------------------------------------------------------------------
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...
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 = 0.4378 r_free = 0.4378 target = 0.207613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.199695 restraints weight = 8977.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.169586 restraints weight = 14174.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.172059 restraints weight = 11885.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172135 restraints weight = 10059.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172135 restraints weight = 9559.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8082  Z= 0.146
  Angle     :  0.623  17.882  11148  Z= 0.310
  Chirality :  0.045   0.346   1377
  Planarity :  0.005   0.052   1464
  Dihedral  :  4.442  17.036   1191
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.20 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  8.19 %
    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 are not related in a simple way.
  whole:  1.60 (0.24), residues: 1134
  helix:  3.01 (0.21), residues: 522
  sheet:  0.84 (0.38), residues: 144
  loop : -1.25 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 815 
 TYR   0.016   0.002   TYR C1067 
 PHE   0.014   0.002   PHE C 782 
 TRP   0.009   0.001   TRP A1102 
 HIS   0.006   0.001   HIS A1064 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.14 ( 8055)
  covalent geometry    : angle       0.56515 /  0.30 (11076)
  SS BOND              : bond        0.00373 /  0.25 (    9)
  SS BOND              : angle       1.13135 /  0.63 (   18)
  hydrogen bonds       : bond        0.04483 /  3.17 (  516)
  hydrogen bonds       : angle       4.38762 /  3.19 ( 1512)
  link_NAG-ASN         : bond        0.01113 /  0.87 (   18)
  link_NAG-ASN         : angle       3.75110 /  2.51 (   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
  95 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  902 MET cc_start: 0.7149 (mmm) cc_final: 0.6415 (tpt)
REVERT: C 1027 THR cc_start: 0.7544 (m) cc_final: 0.7196 (p)
  outliers start: 12
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0682
  time to fit residues: 8.9540
Evaluate side-chains
  77 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 804 GLN
B 928 ASN
B1119 ASN
C1119 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.134277 restraints weight = 9038.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.136827 restraints weight = 9050.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.138716 restraints weight = 7038.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138751 restraints weight = 5375.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139286 restraints weight = 4692.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086   8082  Z= 0.225
  Angle     :  0.717  16.385  11148  Z= 0.354
  Chirality :  0.048   0.254   1377
  Planarity :  0.005   0.031   1464
  Dihedral  :  4.808  22.453   1191
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.97 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 10.80 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.24), residues: 1134
  helix:  3.25 (0.21), residues: 516
  sheet: -0.15 (0.37), residues: 150
  loop : -1.38 (0.24), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 815 
 TYR   0.021   0.002   TYR C1067 
 PHE   0.029   0.002   PHE B 906 
 TRP   0.014   0.003   TRP A1102 
 HIS   0.005   0.001   HIS C1064 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00559 /  0.22 ( 8055)
  covalent geometry    : angle       0.66330 /  0.34 (11076)
  SS BOND              : bond        0.00752 /  0.51 (    9)
  SS BOND              : angle       1.27484 /  0.77 (   18)
  hydrogen bonds       : bond        0.04580 /  3.21 (  516)
  hydrogen bonds       : angle       4.33332 /  3.18 ( 1512)
  link_NAG-ASN         : bond        0.00663 /  0.52 (   18)
  link_NAG-ASN         : angle       3.90776 /  2.58 (   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
  90 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  794 ILE cc_start: 0.6138 (mt) cc_final: 0.5499 (tt)
REVERT: A  822 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6905 (mp)
REVERT: A 1023 ASN cc_start: 0.6579 (m-40) cc_final: 0.6373 (m-40)
REVERT: B  779 GLN cc_start: 0.7944 (mt0) cc_final: 0.7708 (mm-40)
  outliers start: 17
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0940
  time to fit residues: 11.1929
Evaluate side-chains
  74 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  822 LEU
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  805 ILE
Chi-restraints excluded: chain B residue  865 LEU
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:    0.3980
   chunk 48 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0870
   chunk 33 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0970
   chunk 57 optimal weight:    0.0470
   chunk 61 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.2654

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.182035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134634 restraints weight = 8942.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.138430 restraints weight = 6251.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140642 restraints weight = 4999.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.142487 restraints weight = 4362.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.143407 restraints weight = 3986.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8082  Z= 0.106
  Angle     :  0.547  13.572  11148  Z= 0.268
  Chirality :  0.042   0.198   1377
  Planarity :  0.004   0.031   1464
  Dihedral  :  4.156  17.829   1191
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.20 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.29 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.24), residues: 1134
  helix:  3.35 (0.21), residues: 522
  sheet:  0.77 (0.44), residues: 108
  loop : -1.23 (0.24), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 815 
 TYR   0.022   0.001   TYR C1067 
 PHE   0.012   0.001   PHE B 823 
 TRP   0.007   0.001   TRP B1102 
 HIS   0.004   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.11 ( 8055)
  covalent geometry    : angle       0.50839 /  0.26 (11076)
  SS BOND              : bond        0.00258 /  0.18 (    9)
  SS BOND              : angle       0.76569 /  0.44 (   18)
  hydrogen bonds       : bond        0.03680 /  2.61 (  516)
  hydrogen bonds       : angle       3.94835 /  2.88 ( 1512)
  link_NAG-ASN         : bond        0.00535 /  0.42 (   18)
  link_NAG-ASN         : angle       2.92064 /  1.99 (   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
  89 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  822 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6890 (mp)
REVERT: A  900 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7615 (mtm)
REVERT: B  733 LYS cc_start: 0.7979 (pttt) cc_final: 0.7693 (pttp)
REVERT: B  779 GLN cc_start: 0.7798 (mt0) cc_final: 0.7511 (mm-40)
  outliers start: 19
  outliers final: 14
  residues processed: 80
  average time/residue: 0.0711
  time to fit residues: 8.4836
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  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  822 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  900 MET
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  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  729 VAL
Chi-restraints excluded: chain C residue  779 GLN
Chi-restraints excluded: chain C residue  874 THR
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:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0470
   chunk 14 optimal weight:    0.8980
   chunk 97 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    0.7882

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1088 HIS
C1023 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.175403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.133180 restraints weight = 9066.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.129879 restraints weight = 6853.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.132517 restraints weight = 6622.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133423 restraints weight = 5440.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133563 restraints weight = 4757.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8082  Z= 0.154
  Angle     :  0.589  11.960  11148  Z= 0.286
  Chirality :  0.044   0.208   1377
  Planarity :  0.004   0.032   1464
  Dihedral  :  4.208  18.066   1191
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.70 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 13.59 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.24), residues: 1134
  helix:  3.25 (0.21), residues: 528
  sheet: -0.13 (0.37), residues: 144
  loop : -1.19 (0.25), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 815 
 TYR   0.021   0.002   TYR C1067 
 PHE   0.014   0.001   PHE A 906 
 TRP   0.007   0.001   TRP B1102 
 HIS   0.004   0.001   HIS C1064 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.15 ( 8055)
  covalent geometry    : angle       0.55849 /  0.28 (11076)
  SS BOND              : bond        0.00458 /  0.29 (    9)
  SS BOND              : angle       1.01808 /  0.60 (   18)
  hydrogen bonds       : bond        0.03791 /  2.68 (  516)
  hydrogen bonds       : angle       3.91354 /  2.87 ( 1512)
  link_NAG-ASN         : bond        0.00471 /  0.37 (   18)
  link_NAG-ASN         : angle       2.71857 /  1.84 (   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
  88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6709 (mp)
REVERT: A  869 MET cc_start: 0.6311 (mmm) cc_final: 0.5969 (mtp)
REVERT: B  733 LYS cc_start: 0.7798 (pttt) cc_final: 0.7519 (pttp)
REVERT: B  779 GLN cc_start: 0.7826 (mt0) cc_final: 0.7508 (mm-40)
REVERT: C  779 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7693 (mm-40)
  outliers start: 20
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0877
  time to fit residues: 10.1068
Evaluate side-chains
  79 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 60
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  822 LEU
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  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  729 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:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   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:    0.0470
   chunk 81 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.6682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C1088 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.177958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.140462 restraints weight = 8629.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.143484 restraints weight = 6420.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.145245 restraints weight = 5222.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.146557 restraints weight = 4559.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.147309 restraints weight = 4180.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.5234

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= 0.133
  Angle     :  0.560  11.040  11148  Z= 0.271
  Chirality :  0.043   0.244   1377
  Planarity :  0.004   0.030   1464
  Dihedral  :  4.070  17.677   1191
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  2.82 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 13.97 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.24), residues: 1134
  helix:  3.31 (0.21), residues: 528
  sheet: -0.21 (0.37), residues: 144
  loop : -1.16 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 815 
 TYR   0.022   0.001   TYR C1067 
 PHE   0.012   0.001   PHE A1121 
 TRP   0.005   0.001   TRP B1102 
 HIS   0.003   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.13 ( 8055)
  covalent geometry    : angle       0.53613 /  0.27 (11076)
  SS BOND              : bond        0.00332 /  0.19 (    9)
  SS BOND              : angle       0.88420 /  0.52 (   18)
  hydrogen bonds       : bond        0.03615 /  2.55 (  516)
  hydrogen bonds       : angle       3.81570 /  2.81 ( 1512)
  link_NAG-ASN         : bond        0.00423 /  0.33 (   18)
  link_NAG-ASN         : angle       2.35816 /  1.59 (   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
  88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 65
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  822 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6838 (mp)
REVERT: A  869 MET cc_start: 0.6187 (mmm) cc_final: 0.5889 (mtp)
REVERT: B  779 GLN cc_start: 0.7932 (mt0) cc_final: 0.7583 (mm-40)
REVERT: B  823 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7109 (m-80)
REVERT: C  779 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7783 (mm-40)
  outliers start: 23
  outliers final: 16
  residues processed: 78
  average time/residue: 0.0773
  time to fit residues: 8.5247
Evaluate side-chains
  82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  822 LEU
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  823 PHE
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 3 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 59 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 14 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 804 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.188514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.179858 restraints weight = 8326.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.178602 restraints weight = 12912.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.157794 restraints weight = 14642.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.157049 restraints weight = 14930.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.156283 restraints weight = 16134.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8082  Z= 0.149
  Angle     :  0.577   9.591  11148  Z= 0.281
  Chirality :  0.044   0.275   1377
  Planarity :  0.004   0.040   1464
  Dihedral  :  4.157  18.050   1191
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.62 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 13.59 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.25), residues: 1134
  helix:  3.30 (0.21), residues: 528
  sheet: -0.23 (0.37), residues: 144
  loop : -1.25 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 815 
 TYR   0.021   0.002   TYR C1067 
 PHE   0.013   0.001   PHE C1121 
 TRP   0.005   0.001   TRP B1102 
 HIS   0.003   0.001   HIS C1064 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 8055)
  covalent geometry    : angle       0.55625 /  0.28 (11076)
  SS BOND              : bond        0.00414 /  0.25 (    9)
  SS BOND              : angle       1.01121 /  0.60 (   18)
  hydrogen bonds       : bond        0.03678 /  2.60 (  516)
  hydrogen bonds       : angle       3.83873 /  2.82 ( 1512)
  link_NAG-ASN         : bond        0.00419 /  0.32 (   18)
  link_NAG-ASN         : angle       2.23112 /  1.50 (   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: 22
    poor density    : 63
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6953 (mp)
REVERT: A  869 MET cc_start: 0.6074 (mmm) cc_final: 0.5745 (mtp)
REVERT: B  779 GLN cc_start: 0.7893 (mt0) cc_final: 0.7583 (mm-40)
REVERT: B  823 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7314 (m-80)
REVERT: C  779 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7880 (mm-40)
  outliers start: 22
  outliers final: 19
  residues processed: 79
  average time/residue: 0.0832
  time to fit residues: 9.3299
Evaluate side-chains
  81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  822 LEU
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  722 VAL
Chi-restraints excluded: chain B residue  729 VAL
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  823 PHE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue 1104 VAL
Chi-restraints excluded: chain C residue  729 VAL
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:    0.7980
   chunk 22 optimal weight:    0.1980
   chunk 96 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 97 optimal weight:   20.0000
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.7982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.188657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.180101 restraints weight = 8310.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.177413 restraints weight = 13145.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.176325 restraints weight = 17377.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.174321 restraints weight = 19334.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.174034 restraints weight = 19089.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8082  Z= 0.148
  Angle     :  0.576  11.869  11148  Z= 0.280
  Chirality :  0.044   0.299   1377
  Planarity :  0.004   0.032   1464
  Dihedral  :  4.155  17.905   1191
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.26 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 14.34 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.24), residues: 1134
  helix:  3.31 (0.21), residues: 510
  sheet: -0.32 (0.37), residues: 144
  loop : -1.29 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 815 
 TYR   0.022   0.002   TYR C1067 
 PHE   0.013   0.001   PHE C1121 
 TRP   0.006   0.002   TRP C 886 
 HIS   0.003   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 8055)
  covalent geometry    : angle       0.55694 /  0.28 (11076)
  SS BOND              : bond        0.00410 /  0.25 (    9)
  SS BOND              : angle       0.98084 /  0.58 (   18)
  hydrogen bonds       : bond        0.03656 /  2.58 (  516)
  hydrogen bonds       : angle       3.87301 /  2.85 ( 1512)
  link_NAG-ASN         : bond        0.00401 /  0.31 (   18)
  link_NAG-ASN         : angle       2.15489 /  1.44 (   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
  88 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  822 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7010 (mp)
REVERT: A  869 MET cc_start: 0.5526 (mmm) cc_final: 0.5228 (mtp)
  outliers start: 24
  outliers final: 19
  residues processed: 81
  average time/residue: 0.0752
  time to fit residues: 8.9255
Evaluate side-chains
  81 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  822 LEU
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0060
   chunk 36 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 34 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 59 optimal weight:   20.0000
   chunk 110 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0020
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.3164

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.179866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.142295 restraints weight = 8610.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.145069 restraints weight = 6310.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.146869 restraints weight = 5149.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.148364 restraints weight = 4515.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.148790 restraints weight = 4128.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.5668

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= 0.102
  Angle     :  0.538  12.664  11148  Z= 0.257
  Chirality :  0.043   0.309   1377
  Planarity :  0.003   0.032   1464
  Dihedral  :  3.883  16.985   1191
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.00 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.90 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.24), residues: 1134
  helix:  3.40 (0.21), residues: 510
  sheet:  0.27 (0.42), residues: 114
  loop : -1.16 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 815 
 TYR   0.019   0.001   TYR C1067 
 PHE   0.013   0.001   PHE A 823 
 TRP   0.006   0.001   TRP C 886 
 HIS   0.003   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.10 ( 8055)
  covalent geometry    : angle       0.52345 /  0.25 (11076)
  SS BOND              : bond        0.00225 /  0.13 (    9)
  SS BOND              : angle       0.71200 /  0.41 (   18)
  hydrogen bonds       : bond        0.03421 /  2.42 (  516)
  hydrogen bonds       : angle       3.71598 /  2.72 ( 1512)
  link_NAG-ASN         : bond        0.00382 /  0.29 (   18)
  link_NAG-ASN         : angle       1.84969 /  1.25 (   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
  82 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6824 (mp)
REVERT: A  869 MET cc_start: 0.6165 (mmm) cc_final: 0.5877 (mtp)
  outliers start: 18
  outliers final: 17
  residues processed: 79
  average time/residue: 0.0759
  time to fit residues: 8.7497
Evaluate side-chains
  76 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  822 LEU
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  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:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.3980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.192923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.184466 restraints weight = 8194.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.166926 restraints weight = 13227.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.164117 restraints weight = 13642.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.163958 restraints weight = 12388.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.164582 restraints weight = 10763.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8082  Z= 0.108
  Angle     :  0.537  12.804  11148  Z= 0.258
  Chirality :  0.043   0.325   1377
  Planarity :  0.003   0.029   1464
  Dihedral  :  3.839  17.203   1191
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.00 %
    Favored  : 96.74 %
  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 are not related in a simple way.
  whole:  1.76 (0.24), residues: 1134
  helix:  3.42 (0.21), residues: 510
  sheet:  0.27 (0.41), residues: 114
  loop : -1.09 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 815 
 TYR   0.018   0.001   TYR C1067 
 PHE   0.011   0.001   PHE A1121 
 TRP   0.006   0.001   TRP C 886 
 HIS   0.003   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 ( 8055)
  covalent geometry    : angle       0.52379 /  0.26 (11076)
  SS BOND              : bond        0.00266 /  0.15 (    9)
  SS BOND              : angle       0.76039 /  0.44 (   18)
  hydrogen bonds       : bond        0.03389 /  2.41 (  516)
  hydrogen bonds       : angle       3.67772 /  2.70 ( 1512)
  link_NAG-ASN         : bond        0.00379 /  0.29 (   18)
  link_NAG-ASN         : angle       1.74810 /  1.17 (   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  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  822 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6851 (mp)
REVERT: A  869 MET cc_start: 0.5873 (mmm) cc_final: 0.5612 (mtp)
  outliers start: 18
  outliers final: 17
  residues processed: 79
  average time/residue: 0.0773
  time to fit residues: 8.8961
Evaluate side-chains
  80 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    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  819 GLU
Chi-restraints excluded: chain A residue  822 LEU
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  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:    0.0970
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0010
   chunk 25 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B1088 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.191237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.182692 restraints weight = 8227.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.177682 restraints weight = 12471.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.177245 restraints weight = 19110.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.176151 restraints weight = 17083.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.175873 restraints weight = 16381.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8082  Z= 0.122
  Angle     :  0.548  12.904  11148  Z= 0.265
  Chirality :  0.044   0.330   1377
  Planarity :  0.003   0.030   1464
  Dihedral  :  3.947  18.608   1191
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.62 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.46 %
    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 are not related in a simple way.
  whole:  1.77 (0.24), residues: 1134
  helix:  3.43 (0.21), residues: 510
  sheet:  0.18 (0.40), residues: 114
  loop : -1.06 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 815 
 TYR   0.019   0.001   TYR C1067 
 PHE   0.011   0.001   PHE A1121 
 TRP   0.005   0.001   TRP B 886 
 HIS   0.003   0.001   HIS C1101 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 ( 8055)
  covalent geometry    : angle       0.53470 /  0.26 (11076)
  SS BOND              : bond        0.00316 /  0.19 (    9)
  SS BOND              : angle       0.87386 /  0.51 (   18)
  hydrogen bonds       : bond        0.03454 /  2.45 (  516)
  hydrogen bonds       : angle       3.69903 /  2.71 ( 1512)
  link_NAG-ASN         : bond        0.00372 /  0.28 (   18)
  link_NAG-ASN         : angle       1.73490 /  1.15 (   54)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1605.03 seconds
wall clock time: 28 minutes 10.51 seconds (1690.51 seconds total)