Starting phenix.real_space_refine
on Fri Aug 22 16:42:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r7j_18977/08_2025/8r7j_18977.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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      42      5.16       5
     C    3866      2.51       5
     N    1029      2.21       5
     O    1105      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6042
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2658
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 15, 'TRANS': 322}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2955
          Classifications: {'peptide': 364}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 11, 'TRANS': 352}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 429
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 1.54, per 1000 atoms: 0.25
  Number of scatterers: 6042
  At special positions: 0
  Unit cell: (62.267, 106.994, 108.748, 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      42     16.00
     O    1105      8.00
     N    1029      7.00
     C    3866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  68 " - pdb=" SG  CYS B  83 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 229.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1458

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      61.0% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 644 through 653
    Processing helix  chain 'A' and resid 693 through 707
      removed outlier: 3.738A  pdb=" N   GLN A 707 " --> pdb=" O   TYR A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 736
      removed outlier: 4.674A  pdb=" N   TYR A 720 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ASP A 721 " --> pdb=" O   ARG A 717 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A 736 " --> pdb=" O   LYS A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 762
      removed outlier: 3.615A  pdb=" N   SER A 746 " --> pdb=" O   PRO A 742 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 743 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   CYS A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   HIS A 760 " --> pdb=" O   ILE A 756 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   MET A 762 " --> pdb=" O   CYS A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 797
      removed outlier: 3.536A  pdb=" N   ASN A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR A 780 " --> pdb=" O   ASN A 776 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LYS A 781 " --> pdb=" O   GLU A 777 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLN A 791 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU A 793 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 814
      removed outlier: 4.484A  pdb=" N   PHE A 806 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLN A 807 " --> pdb=" O   GLU A 803 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   GLY A 808 " --> pdb=" O   ALA A 804 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR A 809 " --> pdb=" O   GLU A 805 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A 814 " --> pdb=" O   ASN A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 825
      removed outlier: 3.767A  pdb=" N   GLU A 823 " --> pdb=" O   ASP A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 833
    Processing helix  chain 'A' and resid 836 through 849
    Processing helix  chain 'A' and resid 852 through 860
      removed outlier: 4.344A  pdb=" N   LEU A 858 " --> pdb=" O   ARG A 854 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLN A 860 " --> pdb=" O   PHE A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 870
      removed outlier: 3.719A  pdb=" N   LEU A 870 " --> pdb=" O   ASN A 866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 883
      removed outlier: 3.888A  pdb=" N   LYS A 879 " --> pdb=" O   SER A 875 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A 882 " --> pdb=" O   ARG A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 908
    Processing helix  chain 'A' and resid 912 through 924
      removed outlier: 3.510A  pdb=" N   ALA A 916 " --> pdb=" O   ASP A 912 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP A 918 " --> pdb=" O   GLU A 914 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   CYS A 922 " --> pdb=" O   ASP A 918 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   HIS A 923 " --> pdb=" O   PHE A 919 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY A 924 " --> pdb=" O   LEU A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 962 through 968
      removed outlier: 4.346A  pdb=" N   VAL A 966 " --> pdb=" O   VAL A 962 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN A 967 " --> pdb=" O   GLY A 963 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 19
    Processing helix  chain 'B' and resid 23 through 28
    Processing helix  chain 'B' and resid 47 through 54
    Processing helix  chain 'B' and resid 55 through 74
      removed outlier: 5.152A  pdb=" N   MET B  61 " --> pdb=" O   PRO B  57 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   PHE B  62 " --> pdb=" O   TYR B  58 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN B  74 " --> pdb=" O   TYR B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 97
    Processing helix  chain 'B' and resid 104 through 113
      removed outlier: 3.565A  pdb=" N   TYR B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA B 110 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ALA B 112 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU B 113 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 121
      removed outlier: 4.007A  pdb=" N   VAL B 117 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 118 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   ALA B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN B 121 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 153
      removed outlier: 3.606A  pdb=" N   CYS B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL B 151 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 183
      removed outlier: 3.737A  pdb=" N   GLN B 174 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS B 177 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR B 179 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS B 181 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASN B 183 " --> pdb=" O   TYR B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 197
      removed outlier: 4.533A  pdb=" N   ILE B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 222
      removed outlier: 3.533A  pdb=" N   VAL B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   THR B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   TYR B 212 " --> pdb=" O   GLN B 208 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   LYS B 213 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR B 214 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   TYR B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 239
      removed outlier: 3.996A  pdb=" N   ALA B 236 " --> pdb=" O   TYR B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 263
      removed outlier: 3.670A  pdb=" N   TYR B 254 " --> pdb=" O   MET B 250 " (cutoff:3.500A)
      Proline residue:  B 257  - end of helix
    Processing helix  chain 'B' and resid 267 through 274
      removed outlier: 4.195A  pdb=" N   LEU B 271 " --> pdb=" O   THR B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 288
      removed outlier: 3.696A  pdb=" N   SER B 287 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 301
      removed outlier: 3.994A  pdb=" N   HIS B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 317 through 334
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 356 through 370
      removed outlier: 3.515A  pdb=" N   VAL B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN B 361 " --> pdb=" O   ILE B 357 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU B 364 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA B 365 " --> pdb=" O   GLN B 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 60
      removed outlier: 3.648A  pdb=" N   GLU C  59 " --> pdb=" O   GLN C  55 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 899 through 900
    Processing sheet with id=AA2, first strand: chain 'B' and resid 337 through 339
      removed outlier: 3.558A  pdb=" N   VAL B 385 " --> pdb=" O   TYR B 376 " (cutoff:3.500A)

    249 hydrogen bonds defined for protein.
    741 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: 0.80

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1850
        1.34 -     1.46: 1328
        1.46 -     1.58: 2932
        1.58 -     1.70: 1
        1.70 -     1.82: 62
  Bond restraints: 6173
  Sorted by residual:
  bond pdb=" C   LYS B 189 "
       pdb=" N   PRO B 190 "
    ideal  model  delta    sigma   weight residual
    1.336  1.394 -0.058 1.25e-02 6.40e+03 2.16e+01
  bond pdb=" C   PRO B  56 "
       pdb=" N   PRO B  57 "
    ideal  model  delta    sigma   weight residual
    1.336  1.369 -0.033 1.25e-02 6.40e+03 6.90e+00
  bond pdb=" CA  THR A 664 "
       pdb=" CB  THR A 664 "
    ideal  model  delta    sigma   weight residual
    1.518  1.567 -0.050 2.08e-02 2.31e+03 5.71e+00
  bond pdb=" CB  ARG B 323 "
       pdb=" CG  ARG B 323 "
    ideal  model  delta    sigma   weight residual
    1.520  1.585 -0.065 3.00e-02 1.11e+03 4.63e+00
  bond pdb=" N   ASP B 223 "
       pdb=" CA  ASP B 223 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.027 1.29e-02 6.01e+03 4.36e+00
  ... (remaining 6168 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 8133
        3.82 -     7.63: 171
        7.63 -    11.45: 32
       11.45 -    15.26: 4
       15.26 -    19.08: 3
  Bond angle restraints: 8343
  Sorted by residual:
  angle pdb=" C   HIS B 264 "
        pdb=" N   MET B 265 "
        pdb=" CA  MET B 265 "
      ideal   model   delta    sigma   weight residual
     120.68  138.05  -17.37 1.52e+00 4.33e-01 1.31e+02
  angle pdb=" C   HIS B 239 "
        pdb=" N   CYS B 240 "
        pdb=" CA  CYS B 240 "
      ideal   model   delta    sigma   weight residual
     121.54  134.17  -12.63 1.91e+00 2.74e-01 4.38e+01
  angle pdb=" CB  MET B 221 "
        pdb=" CG  MET B 221 "
        pdb=" SD  MET B 221 "
      ideal   model   delta    sigma   weight residual
     112.70  131.78  -19.08 3.00e+00 1.11e-01 4.04e+01
  angle pdb=" N   VAL A 927 "
        pdb=" CA  VAL A 927 "
        pdb=" C   VAL A 927 "
      ideal   model   delta    sigma   weight residual
     112.43  107.01    5.42 9.20e-01 1.18e+00 3.47e+01
  angle pdb=" C   ALA A 672 "
        pdb=" N   VAL A 673 "
        pdb=" CA  VAL A 673 "
      ideal   model   delta    sigma   weight residual
     120.35  128.14   -7.79 1.39e+00 5.18e-01 3.14e+01
  ... (remaining 8338 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 3255
       17.51 -    35.01: 368
       35.01 -    52.51: 76
       52.51 -    70.02: 12
       70.02 -    87.52: 5
  Dihedral angle restraints: 3716
    sinusoidal: 1484
      harmonic: 2232
  Sorted by residual:
  dihedral pdb=" CB  CYS B  68 "
           pdb=" SG  CYS B  68 "
           pdb=" SG  CYS B  83 "
           pdb=" CB  CYS B  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.75  -49.25     1      1.00e+01 1.00e-02 3.33e+01
  dihedral pdb=" CA  PRO A 688 "
           pdb=" C   PRO A 688 "
           pdb=" N   HIS A 689 "
           pdb=" CA  HIS A 689 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.55   25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ILE B 310 "
           pdb=" C   ILE B 310 "
           pdb=" N   PHE B 311 "
           pdb=" CA  PHE B 311 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.78  -25.22     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 3713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 727
       0.068 -    0.136: 160
       0.136 -    0.204: 31
       0.204 -    0.272: 4
       0.272 -    0.340: 4
  Chirality restraints: 926
  Sorted by residual:
  chirality pdb=" CB  VAL A 824 "
            pdb=" CA  VAL A 824 "
            pdb=" CG1 VAL A 824 "
            pdb=" CG2 VAL A 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CA  ASP B 223 "
            pdb=" N   ASP B 223 "
            pdb=" C   ASP B 223 "
            pdb=" CB  ASP B 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" CB  ILE B 178 "
            pdb=" CA  ILE B 178 "
            pdb=" CG1 ILE B 178 "
            pdb=" CG2 ILE B 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 923 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 349 "    0.023 2.00e-02 2.50e+03   3.03e-02 1.61e+01
        pdb=" CG  PHE B 349 "   -0.070 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 349 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 349 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 349 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 349 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 349 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  33 "    0.057 5.00e-02 4.00e+02   8.59e-02 1.18e+01
        pdb=" N   PRO B  34 "   -0.149 5.00e-02 4.00e+02
        pdb=" CA  PRO B  34 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B  34 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 392 "   -0.055 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO B 393 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO B 393 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 393 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1434
        2.79 -     3.32: 5342
        3.32 -     3.85: 9491
        3.85 -     4.37: 10482
        4.37 -     4.90: 17722
  Nonbonded interactions: 44471
  Sorted by model distance:
  nonbonded pdb=" O   THR A 917 "
            pdb=" OG1 THR A 921 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" OG  SER B 387 "
            pdb=" O   ASN B 390 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ALA B 280 "
            pdb=" OG1 THR B 283 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ARG A 731 "
            pdb=" OG1 THR A 735 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" O   TYR A 889 "
            pdb=" OG1 THR A 897 "
     model   vdw
     2.318 3.040
  ... (remaining 44466 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.200
  Find NCS groups from input model:        0.030
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
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      :  0.006   0.065   6174  Z= 0.305
  Angle     :  1.378  19.077   8345  Z= 0.743
  Chirality :  0.063   0.340    926
  Planarity :  0.009   0.089   1071
  Dihedral  : 15.423  87.522   2255
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.10 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.77 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.73 (0.22), residues: 738
  helix: -2.95 (0.18), residues: 435
  sheet: -2.37 (1.19), residues: 10
  loop : -3.29 (0.27), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG B 193 
 TYR   0.021   0.002   TYR B 204 
 PHE   0.070   0.004   PHE B 349 
 TRP   0.056   0.004   TRP B 103 
 HIS   0.017   0.002   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 ( 6173)
  covalent geometry    : angle       1.37671 ( 8343)
  SS BOND              : bond        0.00450 (    1)
  SS BOND              : angle       3.40735 (    2)
  hydrogen bonds       : bond        0.20972 (  249)
  hydrogen bonds       : angle       8.10895 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 171
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  690 GLU cc_start: 0.7182 (pt0) cc_final: 0.6777 (tp30)
REVERT: A  747 LEU cc_start: 0.8518 (mm) cc_final: 0.8146 (mm)
REVERT: A  751 CYS cc_start: 0.7991 (m) cc_final: 0.7766 (m)
REVERT: A  788 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8209 (mt-10)
REVERT: A  803 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: A  819 ASP cc_start: 0.7510 (m-30) cc_final: 0.6856 (t70)
REVERT: A  868 CYS cc_start: 0.7970 (p) cc_final: 0.7218 (m)
REVERT: A  902 ASP cc_start: 0.7051 (t0) cc_final: 0.6846 (t0)
REVERT: A  912 ASP cc_start: 0.7577 (p0) cc_final: 0.7033 (p0)
REVERT: B   85 THR cc_start: 0.8582 (m) cc_final: 0.8294 (p)
REVERT: B  137 MET cc_start: 0.6701 (pmm) cc_final: 0.6039 (pmm)
REVERT: B  261 LEU cc_start: 0.7844 (mm) cc_final: 0.7620 (mm)
REVERT: B  350 MET cc_start: 0.6778 (mmp) cc_final: 0.6573 (mmp)
  outliers start: 2
  outliers final: 1
  residues processed: 172
  average time/residue: 0.0740
  time to fit residues: 17.2934
Evaluate side-chains
  128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  810 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0000
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
B 186 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.156648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.132810 restraints weight = 13010.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.136336 restraints weight = 6637.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.138663 restraints weight = 4192.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.140263 restraints weight = 3034.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.141231 restraints weight = 2405.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6174  Z= 0.136
  Angle     :  0.709   9.527   8345  Z= 0.362
  Chirality :  0.041   0.230    926
  Planarity :  0.006   0.079   1071
  Dihedral  :  5.851  59.412    812
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  5.42 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.73 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.27), residues: 738
  helix: -1.49 (0.22), residues: 446
  sheet: -2.96 (0.89), residues: 20
  loop : -3.04 (0.31), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 193 
 TYR   0.023   0.002   TYR B   9 
 PHE   0.018   0.001   PHE C  52 
 TRP   0.016   0.001   TRP B 103 
 HIS   0.004   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6173)
  covalent geometry    : angle       0.70803 ( 8343)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       2.37792 (    2)
  hydrogen bonds       : bond        0.04718 (  249)
  hydrogen bonds       : angle       5.01631 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  751 CYS cc_start: 0.7953 (m) cc_final: 0.7745 (m)
REVERT: A  788 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8245 (mt-10)
REVERT: A  803 GLU cc_start: 0.7345 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: A  819 ASP cc_start: 0.7488 (m-30) cc_final: 0.6908 (t70)
REVERT: A  868 CYS cc_start: 0.7801 (p) cc_final: 0.7241 (m)
REVERT: B  137 MET cc_start: 0.6789 (pmm) cc_final: 0.6302 (pmm)
REVERT: B  327 LYS cc_start: 0.7759 (ttmt) cc_final: 0.7329 (tptm)
  outliers start: 12
  outliers final: 6
  residues processed: 139
  average time/residue: 0.0654
  time to fit residues: 12.3411
Evaluate side-chains
  119 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0000
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0980
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 372 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.154819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.131045 restraints weight = 13128.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.134589 restraints weight = 6840.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.136940 restraints weight = 4351.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.138526 restraints weight = 3159.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.139484 restraints weight = 2512.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6174  Z= 0.116
  Angle     :  0.621   8.113   8345  Z= 0.319
  Chirality :  0.039   0.163    926
  Planarity :  0.005   0.077   1071
  Dihedral  :  4.820  22.828    810
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.56 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.87 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.29), residues: 738
  helix: -0.64 (0.24), residues: 445
  sheet: -2.74 (0.92), residues: 20
  loop : -2.66 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 218 
 TYR   0.019   0.001   TYR B   9 
 PHE   0.013   0.001   PHE A 722 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.004   0.001   HIS B  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6173)
  covalent geometry    : angle       0.62053 ( 8343)
  SS BOND              : bond        0.00316 (    1)
  SS BOND              : angle       1.90710 (    2)
  hydrogen bonds       : bond        0.04019 (  249)
  hydrogen bonds       : angle       4.43544 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  751 CYS cc_start: 0.8036 (m) cc_final: 0.7833 (m)
REVERT: A  788 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8220 (mt-10)
REVERT: A  819 ASP cc_start: 0.7539 (m-30) cc_final: 0.6917 (t70)
REVERT: A  868 CYS cc_start: 0.7984 (p) cc_final: 0.7247 (m)
REVERT: B   91 PHE cc_start: 0.8369 (t80) cc_final: 0.7690 (t80)
REVERT: B  137 MET cc_start: 0.6498 (pmm) cc_final: 0.6239 (pmm)
  outliers start: 16
  outliers final: 13
  residues processed: 133
  average time/residue: 0.0490
  time to fit residues: 9.3231
Evaluate side-chains
  126 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0020
   chunk 54 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.153655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129582 restraints weight = 13385.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.133177 restraints weight = 6988.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.135542 restraints weight = 4474.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.137106 restraints weight = 3266.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.138175 restraints weight = 2611.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6174  Z= 0.112
  Angle     :  0.594  10.922   8345  Z= 0.303
  Chirality :  0.039   0.161    926
  Planarity :  0.004   0.065   1071
  Dihedral  :  4.546  22.916    810
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.15 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.40 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.65 (0.30), residues: 738
  helix: -0.23 (0.24), residues: 446
  sheet: -2.49 (0.98), residues: 20
  loop : -2.39 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 218 
 TYR   0.017   0.001   TYR B   9 
 PHE   0.015   0.001   PHE A 770 
 TRP   0.007   0.001   TRP B 103 
 HIS   0.004   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6173)
  covalent geometry    : angle       0.59379 ( 8343)
  SS BOND              : bond        0.00324 (    1)
  SS BOND              : angle       1.88276 (    2)
  hydrogen bonds       : bond        0.03646 (  249)
  hydrogen bonds       : angle       4.26083 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8236 (mt-10)
REVERT: A  806 PHE cc_start: 0.6766 (m-10) cc_final: 0.6384 (m-80)
REVERT: A  819 ASP cc_start: 0.7631 (m-30) cc_final: 0.6986 (t70)
REVERT: A  868 CYS cc_start: 0.8093 (p) cc_final: 0.7366 (m)
REVERT: B    8 GLN cc_start: 0.8539 (mp10) cc_final: 0.8106 (pt0)
REVERT: B   61 MET cc_start: 0.7825 (mmm) cc_final: 0.7429 (mmm)
REVERT: B   91 PHE cc_start: 0.8339 (t80) cc_final: 0.7518 (t80)
REVERT: B  137 MET cc_start: 0.6444 (pmm) cc_final: 0.6204 (pmm)
REVERT: B  260 MET cc_start: 0.8299 (mmm) cc_final: 0.7947 (mmm)
REVERT: C   25 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7557 (mm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 141
  average time/residue: 0.0580
  time to fit residues: 11.6643
Evaluate side-chains
  136 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  824 VAL
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  890 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 68 optimal weight:    2.9990
   chunk 61 optimal weight:    0.3980
   chunk 16 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.150935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.126403 restraints weight = 13461.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.129940 restraints weight = 7139.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.132305 restraints weight = 4610.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.133875 restraints weight = 3365.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.134985 restraints weight = 2693.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6174  Z= 0.126
  Angle     :  0.606   9.217   8345  Z= 0.306
  Chirality :  0.040   0.173    926
  Planarity :  0.005   0.062   1071
  Dihedral  :  4.460  22.071    810
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.96 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.17 %
    Favored  : 76.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.31), residues: 738
  helix:  0.07 (0.25), residues: 443
  sheet: -2.45 (1.04), residues: 20
  loop : -2.15 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  93 
 TYR   0.018   0.001   TYR B 204 
 PHE   0.015   0.001   PHE A 770 
 TRP   0.006   0.001   TRP B 166 
 HIS   0.005   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6173)
  covalent geometry    : angle       0.60507 ( 8343)
  SS BOND              : bond        0.00356 (    1)
  SS BOND              : angle       1.99912 (    2)
  hydrogen bonds       : bond        0.03751 (  249)
  hydrogen bonds       : angle       4.27946 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8453 (mp)
REVERT: A  788 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8276 (mt-10)
REVERT: A  803 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: A  819 ASP cc_start: 0.7577 (m-30) cc_final: 0.6967 (t70)
REVERT: B    8 GLN cc_start: 0.8556 (mp10) cc_final: 0.8101 (pt0)
  outliers start: 25
  outliers final: 23
  residues processed: 135
  average time/residue: 0.0526
  time to fit residues: 10.3033
Evaluate side-chains
  138 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  890 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 689 HIS
B  52 GLN
B  65 HIS
B 208 GLN
B 351 GLN
C  47 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.150253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126116 restraints weight = 13225.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.129595 restraints weight = 6974.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.131891 restraints weight = 4483.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.133469 restraints weight = 3281.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134542 restraints weight = 2623.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.096   6174  Z= 0.119
  Angle     :  0.603   8.474   8345  Z= 0.306
  Chirality :  0.040   0.220    926
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.411  22.397    810
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.56 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 19.33 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.31), residues: 738
  helix:  0.19 (0.25), residues: 444
  sheet: -2.26 (1.10), residues: 20
  loop : -1.94 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 218 
 TYR   0.019   0.001   TYR B 204 
 PHE   0.016   0.001   PHE A 770 
 TRP   0.005   0.001   TRP C  39 
 HIS   0.005   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6173)
  covalent geometry    : angle       0.60238 ( 8343)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       1.91000 (    2)
  hydrogen bonds       : bond        0.03563 (  249)
  hydrogen bonds       : angle       4.27615 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (mp)
REVERT: A  788 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8284 (mt-10)
REVERT: A  819 ASP cc_start: 0.7625 (m-30) cc_final: 0.6993 (t70)
REVERT: B    8 GLN cc_start: 0.8568 (mp10) cc_final: 0.8107 (pt0)
REVERT: B   91 PHE cc_start: 0.8184 (t80) cc_final: 0.7743 (t80)
REVERT: B  204 TYR cc_start: 0.7235 (m-80) cc_final: 0.6929 (m-80)
REVERT: B  250 MET cc_start: 0.7964 (tpp) cc_final: 0.7681 (tpp)
  outliers start: 32
  outliers final: 24
  residues processed: 138
  average time/residue: 0.0523
  time to fit residues: 10.4782
Evaluate side-chains
  143 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  890 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  223 ASP
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain C residue   60 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS
B 183 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.149614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.125450 restraints weight = 13505.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.128969 restraints weight = 6998.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.131308 restraints weight = 4473.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.132819 restraints weight = 3257.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133964 restraints weight = 2618.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   6174  Z= 0.123
  Angle     :  0.608   9.652   8345  Z= 0.308
  Chirality :  0.039   0.128    926
  Planarity :  0.004   0.054   1071
  Dihedral  :  4.350  22.295    810
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.56 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 20.71 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.32), residues: 738
  helix:  0.25 (0.25), residues: 446
  sheet: -2.04 (1.16), residues: 20
  loop : -1.82 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 218 
 TYR   0.019   0.001   TYR B 204 
 PHE   0.015   0.001   PHE A 770 
 TRP   0.006   0.001   TRP C  39 
 HIS   0.006   0.001   HIS A 689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6173)
  covalent geometry    : angle       0.60767 ( 8343)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.99373 (    2)
  hydrogen bonds       : bond        0.03589 (  249)
  hydrogen bonds       : angle       4.29175 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8541 (mp)
REVERT: A  724 TRP cc_start: 0.7351 (t60) cc_final: 0.7126 (t60)
REVERT: A  788 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8279 (mt-10)
REVERT: A  803 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6905 (tm-30)
REVERT: A  819 ASP cc_start: 0.7645 (m-30) cc_final: 0.6982 (t70)
REVERT: B    8 GLN cc_start: 0.8580 (mp10) cc_final: 0.8199 (pt0)
REVERT: B   91 PHE cc_start: 0.8281 (t80) cc_final: 0.7806 (t80)
REVERT: B  108 MET cc_start: 0.8382 (tpt) cc_final: 0.8083 (tmm)
REVERT: B  250 MET cc_start: 0.8021 (tpp) cc_final: 0.7732 (tpp)
REVERT: B  337 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7753 (mt0)
  outliers start: 32
  outliers final: 23
  residues processed: 142
  average time/residue: 0.0457
  time to fit residues: 9.4822
Evaluate side-chains
  143 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  798 VAL
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  890 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  223 ASP
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  337 GLN
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 41 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
B  65 HIS
** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.146580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122643 restraints weight = 12991.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.125951 restraints weight = 7061.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.128172 restraints weight = 4633.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129640 restraints weight = 3443.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.130655 restraints weight = 2802.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   6174  Z= 0.246
  Angle     :  0.776  10.743   8345  Z= 0.392
  Chirality :  0.046   0.190    926
  Planarity :  0.005   0.053   1071
  Dihedral  :  5.143  25.387    810
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.37 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 21.93 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.39 (0.30), residues: 738
  helix: -0.20 (0.24), residues: 443
  sheet: -2.62 (1.09), residues: 20
  loop : -1.90 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 218 
 TYR   0.024   0.002   TYR B 322 
 PHE   0.022   0.003   PHE B  91 
 TRP   0.010   0.002   TRP C  43 
 HIS   0.008   0.002   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 6173)
  covalent geometry    : angle       0.77528 ( 8343)
  SS BOND              : bond        0.00251 (    1)
  SS BOND              : angle       2.34141 (    2)
  hydrogen bonds       : bond        0.04648 (  249)
  hydrogen bonds       : angle       4.96261 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  633 PHE cc_start: 0.7250 (p90) cc_final: 0.7034 (p90)
REVERT: A  788 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8243 (mt-10)
REVERT: A  819 ASP cc_start: 0.7745 (m-30) cc_final: 0.7166 (t0)
REVERT: A  868 CYS cc_start: 0.8237 (p) cc_final: 0.7978 (m)
REVERT: B   91 PHE cc_start: 0.8584 (t80) cc_final: 0.8114 (t80)
REVERT: B  250 MET cc_start: 0.8246 (tpp) cc_final: 0.7940 (tpp)
REVERT: B  254 TYR cc_start: 0.8042 (m-80) cc_final: 0.7667 (m-80)
REVERT: B  337 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7810 (mt0)
  outliers start: 29
  outliers final: 23
  residues processed: 127
  average time/residue: 0.0538
  time to fit residues: 9.9172
Evaluate side-chains
  127 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  890 THR
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  896 SER
Chi-restraints excluded: chain A residue  897 THR
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  223 ASP
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  337 GLN
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0050
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0040
   chunk 56 optimal weight:    0.0670
   chunk 45 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.2344

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

Flipped N/Q/H residues before XYZ refinement:
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
B  65 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.149300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.125780 restraints weight = 13443.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.129300 restraints weight = 6942.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.131592 restraints weight = 4417.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.133152 restraints weight = 3233.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.134231 restraints weight = 2592.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6174  Z= 0.119
  Angle     :  0.655  11.871   8345  Z= 0.325
  Chirality :  0.040   0.147    926
  Planarity :  0.004   0.055   1071
  Dihedral  :  4.511  21.121    810
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.96 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.01 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.32), residues: 738
  helix:  0.11 (0.25), residues: 444
  sheet: -2.29 (1.14), residues: 20
  loop : -1.55 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 218 
 TYR   0.022   0.001   TYR B 214 
 PHE   0.018   0.001   PHE B 349 
 TRP   0.007   0.001   TRP C  43 
 HIS   0.008   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6173)
  covalent geometry    : angle       0.65429 ( 8343)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       1.88597 (    2)
  hydrogen bonds       : bond        0.03583 (  249)
  hydrogen bonds       : angle       4.41006 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  788 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8313 (mt-10)
REVERT: A  819 ASP cc_start: 0.7606 (m-30) cc_final: 0.7084 (t70)
REVERT: B    8 GLN cc_start: 0.8559 (mp10) cc_final: 0.8145 (pt0)
REVERT: B   91 PHE cc_start: 0.8345 (t80) cc_final: 0.7928 (t80)
REVERT: B  108 MET cc_start: 0.8406 (tpt) cc_final: 0.8196 (tmm)
  outliers start: 18
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0541
  time to fit residues: 10.0321
Evaluate side-chains
  131 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 47 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 31 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 810 ASN
** A 923 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 HIS
B 173 ASN
B 183 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.147049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123605 restraints weight = 13418.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.126970 restraints weight = 6969.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129205 restraints weight = 4481.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.130609 restraints weight = 3284.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.131757 restraints weight = 2664.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6174  Z= 0.138
  Angle     :  0.662  11.411   8345  Z= 0.328
  Chirality :  0.041   0.164    926
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.521  22.036    810
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.83 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 23.31 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.31), residues: 738
  helix:  0.13 (0.25), residues: 444
  sheet: -2.32 (1.14), residues: 20
  loop : -1.63 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 218 
 TYR   0.023   0.001   TYR B 204 
 PHE   0.025   0.002   PHE B 349 
 TRP   0.005   0.001   TRP B 166 
 HIS   0.007   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6173)
  covalent geometry    : angle       0.66111 ( 8343)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       1.92525 (    2)
  hydrogen bonds       : bond        0.03656 (  249)
  hydrogen bonds       : angle       4.46233 (  741)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8316 (mt-10)
REVERT: A  819 ASP cc_start: 0.7659 (m-30) cc_final: 0.7139 (t70)
REVERT: B    8 GLN cc_start: 0.8576 (mp10) cc_final: 0.8173 (pt0)
REVERT: B   91 PHE cc_start: 0.8368 (t80) cc_final: 0.7993 (t80)
REVERT: B  108 MET cc_start: 0.8462 (tpt) cc_final: 0.8187 (tmm)
REVERT: B  337 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7770 (mt0)
  outliers start: 19
  outliers final: 16
  residues processed: 123
  average time/residue: 0.0474
  time to fit residues: 8.5001
Evaluate side-chains
  128 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   62 PHE
Chi-restraints excluded: chain B residue   83 CYS
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  326 PHE
Chi-restraints excluded: chain B residue  337 GLN
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 68 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.148605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.125264 restraints weight = 13225.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.128738 restraints weight = 6773.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.131023 restraints weight = 4292.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.132563 restraints weight = 3121.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.133585 restraints weight = 2501.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6174  Z= 0.124
  Angle     :  0.658  11.308   8345  Z= 0.326
  Chirality :  0.040   0.179    926
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.463  21.363    810
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.10 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 23.31 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.31), residues: 738
  helix:  0.10 (0.25), residues: 446
  sheet: -2.26 (1.14), residues: 20
  loop : -1.58 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 218 
 TYR   0.026   0.001   TYR B 204 
 PHE   0.020   0.002   PHE B 349 
 TRP   0.006   0.001   TRP A 724 
 HIS   0.007   0.001   HIS A 757 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6173)
  covalent geometry    : angle       0.65705 ( 8343)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       1.84717 (    2)
  hydrogen bonds       : bond        0.03679 (  249)
  hydrogen bonds       : angle       4.44659 (  741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1133.09 seconds
wall clock time: 20 minutes 9.52 seconds (1209.52 seconds total)