Starting phenix.real_space_refine
on Thu Jul 24 11:07:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r7j_18977/07_2025/8r7j_18977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r7j_18977/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r7j_18977/07_2025/8r7j_18977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r7j_18977/07_2025/8r7j_18977.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r7j_18977/07_2025/8r7j_18977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r7j_18977/07_2025/8r7j_18977.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'HIS:plan': 1}
          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: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 4.07, per 1000 atoms: 0.67
  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: 1.22
  Conformation dependent library (CDL) restraints added in 815.7 milliseconds
  

  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: 0.53
  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: 1.20

  Time building geometry restraints manager: 1.51 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.530
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.980
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.056   0.004   TRP B 103 
 HIS   0.017   0.002   HIS B  98 
 PHE   0.070   0.004   PHE B 349 
 TYR   0.021   0.002   TYR B 204 
 ARG   0.019   0.001   ARG B 193 

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

*********************** 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  : 0.718 
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: 0.7034 (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: 0.1633
  time to fit residues: 37.3759
Evaluate side-chains
  129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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 62 optimal weight:    0.9980
   chunk 56 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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
B 366 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.131424 restraints weight = 12858.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.134873 restraints weight = 6632.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.137176 restraints weight = 4221.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2267

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= 0.144
  Angle     :  0.716  10.286   8345  Z= 0.366
  Chirality :  0.041   0.214    926
  Planarity :  0.006   0.079   1071
  Dihedral  :  5.853  60.597    812
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  5.28 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.88 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.27), residues: 738
  helix: -1.45 (0.22), residues: 446
  sheet: -2.98 (0.91), residues: 20
  loop : -3.00 (0.31), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 103 
 HIS   0.004   0.001   HIS B  33 
 PHE   0.019   0.002   PHE C  52 
 TYR   0.022   0.002   TYR B   9 
 ARG   0.004   0.001   ARG B 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  249)
  hydrogen bonds       : angle       4.98682 (  741)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       2.48008 (    2)
  covalent geometry    : bond        0.00324 ( 6173)
  covalent geometry    : angle       0.71462 ( 8343)

*********************** 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
  146 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  751 CYS cc_start: 0.8075 (m) cc_final: 0.7875 (m)
REVERT: A  788 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8260 (mt-10)
REVERT: A  803 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7195 (tm-30)
REVERT: A  819 ASP cc_start: 0.7621 (m-30) cc_final: 0.6987 (t70)
REVERT: A  868 CYS cc_start: 0.7945 (p) cc_final: 0.7288 (m)
REVERT: B  137 MET cc_start: 0.6827 (pmm) cc_final: 0.6362 (pmm)
REVERT: B  327 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7360 (tptm)
REVERT: B  354 ASP cc_start: 0.6761 (t0) cc_final: 0.6545 (t70)
  outliers start: 13
  outliers final: 8
  residues processed: 139
  average time/residue: 0.1616
  time to fit residues: 30.2818
Evaluate side-chains
  123 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  896 SER
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 29 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS
B 372 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.151780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.127686 restraints weight = 13227.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.131174 restraints weight = 6852.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.133495 restraints weight = 4383.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6174  Z= 0.127
  Angle     :  0.631   7.598   8345  Z= 0.325
  Chirality :  0.040   0.158    926
  Planarity :  0.005   0.077   1071
  Dihedral  :  4.859  22.680    810
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.83 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.94 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.30), residues: 738
  helix: -0.55 (0.24), residues: 442
  sheet: -2.86 (0.94), residues: 20
  loop : -2.58 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 103 
 HIS   0.006   0.001   HIS B  98 
 PHE   0.015   0.002   PHE A 806 
 TYR   0.024   0.001   TYR A 720 
 ARG   0.005   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  249)
  hydrogen bonds       : angle       4.45525 (  741)
  SS BOND              : bond        0.00296 (    1)
  SS BOND              : angle       1.91901 (    2)
  covalent geometry    : bond        0.00284 ( 6173)
  covalent geometry    : angle       0.63058 ( 8343)

*********************** 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
  148 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  751 CYS cc_start: 0.8148 (m) cc_final: 0.7944 (m)
REVERT: A  788 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8242 (mt-10)
REVERT: A  819 ASP cc_start: 0.7710 (m-30) cc_final: 0.7066 (t70)
REVERT: A  868 CYS cc_start: 0.8103 (p) cc_final: 0.7475 (m)
REVERT: B    8 GLN cc_start: 0.8610 (mp10) cc_final: 0.8215 (pt0)
REVERT: B  137 MET cc_start: 0.6667 (pmm) cc_final: 0.6364 (pmm)
REVERT: B  260 MET cc_start: 0.8437 (mmm) cc_final: 0.8064 (mmt)
  outliers start: 20
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1336
  time to fit residues: 25.6465
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  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  744 THR
Chi-restraints excluded: chain A residue  802 SER
Chi-restraints excluded: chain A residue  813 LEU
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   62 PHE
Chi-restraints excluded: chain B residue  105 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0040
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8994

-------------------------------------------------------------------------------
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 = 0.4035 r_free = 0.4035 target = 0.150552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.126255 restraints weight = 13377.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.129791 restraints weight = 6953.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.132162 restraints weight = 4428.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6174  Z= 0.123
  Angle     :  0.608  11.803   8345  Z= 0.312
  Chirality :  0.040   0.152    926
  Planarity :  0.004   0.064   1071
  Dihedral  :  4.700  22.991    810
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.88 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 18.25 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.31), residues: 738
  helix: -0.13 (0.25), residues: 443
  sheet: -2.80 (0.97), residues: 20
  loop : -2.10 (0.38), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  39 
 HIS   0.005   0.001   HIS A 757 
 PHE   0.014   0.002   PHE A 770 
 TYR   0.017   0.001   TYR B   9 
 ARG   0.003   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03724 (  249)
  hydrogen bonds       : angle       4.35292 (  741)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       1.97908 (    2)
  covalent geometry    : bond        0.00287 ( 6173)
  covalent geometry    : angle       0.60755 ( 8343)

*********************** 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
  151 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8670 (mp)
REVERT: A  788 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8242 (mt-10)
REVERT: A  819 ASP cc_start: 0.7726 (m-30) cc_final: 0.7104 (t70)
REVERT: A  868 CYS cc_start: 0.8114 (p) cc_final: 0.7608 (m)
REVERT: B    8 GLN cc_start: 0.8571 (mp10) cc_final: 0.8099 (pt0)
REVERT: B  137 MET cc_start: 0.6548 (pmm) cc_final: 0.6246 (pmm)
REVERT: C   25 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7619 (mm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 140
  average time/residue: 0.1675
  time to fit residues: 32.8544
Evaluate side-chains
  133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
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  847 LEU
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  223 ASP
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 VAL
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 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0570
   chunk 73 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
A 689 HIS
A 810 ASN
B  65 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.150180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.125966 restraints weight = 13203.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129491 restraints weight = 6942.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.131822 restraints weight = 4461.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6174  Z= 0.120
  Angle     :  0.590   9.531   8345  Z= 0.303
  Chirality :  0.040   0.208    926
  Planarity :  0.004   0.056   1071
  Dihedral  :  4.499  22.172    810
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.02 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.31), residues: 738
  helix:  0.07 (0.25), residues: 444
  sheet: -2.65 (1.07), residues: 20
  loop : -1.96 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 166 
 HIS   0.005   0.001   HIS A 757 
 PHE   0.013   0.001   PHE A 806 
 TYR   0.019   0.001   TYR B 204 
 ARG   0.004   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  249)
  hydrogen bonds       : angle       4.35527 (  741)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       2.00698 (    2)
  covalent geometry    : bond        0.00279 ( 6173)
  covalent geometry    : angle       0.58952 ( 8343)

*********************** 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
  151 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: A  788 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8263 (mt-10)
REVERT: A  819 ASP cc_start: 0.7697 (m-30) cc_final: 0.7086 (t70)
REVERT: B    8 GLN cc_start: 0.8577 (mp10) cc_final: 0.8177 (pt0)
REVERT: B   91 PHE cc_start: 0.8355 (t80) cc_final: 0.7846 (t80)
REVERT: B  137 MET cc_start: 0.6615 (pmm) cc_final: 0.6316 (pmm)
REVERT: B  204 TYR cc_start: 0.7537 (m-80) cc_final: 0.7232 (m-80)
  outliers start: 28
  outliers final: 22
  residues processed: 135
  average time/residue: 0.1912
  time to fit residues: 37.8435
Evaluate side-chains
  143 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
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  847 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  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  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  392 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0170
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0070
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.150072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.125904 restraints weight = 13211.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.129403 restraints weight = 6946.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.131740 restraints weight = 4445.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.4117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.089   6174  Z= 0.118
  Angle     :  0.600   9.935   8345  Z= 0.305
  Chirality :  0.040   0.166    926
  Planarity :  0.004   0.051   1071
  Dihedral  :  4.405  22.696    810
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.15 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 19.63 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.32), residues: 738
  helix:  0.21 (0.25), residues: 446
  sheet: -2.51 (1.09), residues: 20
  loop : -1.82 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  39 
 HIS   0.005   0.001   HIS A 757 
 PHE   0.014   0.001   PHE A 770 
 TYR   0.022   0.001   TYR B 204 
 ARG   0.004   0.000   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  249)
  hydrogen bonds       : angle       4.28590 (  741)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       1.93809 (    2)
  covalent geometry    : bond        0.00301 ( 6173)
  covalent geometry    : angle       0.59883 ( 8343)

*********************** 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
  157 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8586 (mp)
REVERT: A  788 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8291 (mt-10)
REVERT: A  819 ASP cc_start: 0.7587 (m-30) cc_final: 0.6990 (t70)
REVERT: B    8 GLN cc_start: 0.8587 (mp10) cc_final: 0.8193 (pt0)
REVERT: B   91 PHE cc_start: 0.8331 (t80) cc_final: 0.7832 (t80)
REVERT: B  137 MET cc_start: 0.6511 (pmm) cc_final: 0.6306 (pmm)
REVERT: B  204 TYR cc_start: 0.7187 (m-80) cc_final: 0.6882 (m-80)
REVERT: B  250 MET cc_start: 0.8004 (tpp) cc_final: 0.7746 (tpp)
  outliers start: 33
  outliers final: 24
  residues processed: 143
  average time/residue: 0.2158
  time to fit residues: 44.5287
Evaluate side-chains
  144 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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  847 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  904 VAL
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   60 GLU
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  253 ILE
Chi-restraints excluded: chain B residue  258 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
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
B 183 ASN
C  47 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.146365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.122434 restraints weight = 13317.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.125901 restraints weight = 6938.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.128215 restraints weight = 4441.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   6174  Z= 0.152
  Angle     :  0.623   8.347   8345  Z= 0.319
  Chirality :  0.041   0.159    926
  Planarity :  0.004   0.053   1071
  Dihedral  :  4.571  23.021    810
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.96 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 21.17 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.32), residues: 738
  helix:  0.25 (0.25), residues: 444
  sheet: -2.64 (1.11), residues: 20
  loop : -1.70 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  39 
 HIS   0.007   0.001   HIS A 923 
 PHE   0.027   0.002   PHE A 806 
 TYR   0.020   0.002   TYR B 322 
 ARG   0.004   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03897 (  249)
  hydrogen bonds       : angle       4.51571 (  741)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       2.09774 (    2)
  covalent geometry    : bond        0.00366 ( 6173)
  covalent geometry    : angle       0.62203 ( 8343)

*********************** 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
  141 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  704 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8642 (mp)
REVERT: A  788 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8251 (mt-10)
REVERT: A  819 ASP cc_start: 0.7744 (m-30) cc_final: 0.7133 (t70)
REVERT: B   91 PHE cc_start: 0.8504 (t80) cc_final: 0.7905 (t80)
REVERT: B  137 MET cc_start: 0.6498 (pmm) cc_final: 0.6243 (pmm)
REVERT: B  250 MET cc_start: 0.8091 (tpp) cc_final: 0.7824 (tpp)
REVERT: B  254 TYR cc_start: 0.7938 (m-80) cc_final: 0.7662 (m-80)
  outliers start: 28
  outliers final: 22
  residues processed: 130
  average time/residue: 0.1313
  time to fit residues: 24.9357
Evaluate side-chains
  133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
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  813 LEU
Chi-restraints excluded: chain A residue  847 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  904 VAL
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  392 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 689 HIS
B  65 HIS
B 183 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.145833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.121802 restraints weight = 12912.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.125067 restraints weight = 7118.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.127233 restraints weight = 4740.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   6174  Z= 0.237
  Angle     :  0.728  11.417   8345  Z= 0.375
  Chirality :  0.045   0.197    926
  Planarity :  0.005   0.052   1071
  Dihedral  :  5.099  25.393    810
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.83 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 22.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.31), residues: 738
  helix: -0.09 (0.24), residues: 444
  sheet:  None (None), residues: 0
  loop : -1.82 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 166 
 HIS   0.008   0.001   HIS A 757 
 PHE   0.017   0.002   PHE A 806 
 TYR   0.022   0.002   TYR B 322 
 ARG   0.007   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 (  249)
  hydrogen bonds       : angle       4.95580 (  741)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       2.29264 (    2)
  covalent geometry    : bond        0.00564 ( 6173)
  covalent geometry    : angle       0.72760 ( 8343)

*********************** 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
  133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8274 (mt-10)
REVERT: A  803 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: A  819 ASP cc_start: 0.7837 (m-30) cc_final: 0.7349 (t0)
REVERT: B   91 PHE cc_start: 0.8576 (t80) cc_final: 0.8250 (t80)
REVERT: B  137 MET cc_start: 0.6824 (pmm) cc_final: 0.6575 (pmm)
REVERT: B  250 MET cc_start: 0.8200 (tpp) cc_final: 0.7775 (tpp)
  outliers start: 27
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1298
  time to fit residues: 23.1633
Evaluate side-chains
  125 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
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  813 LEU
Chi-restraints excluded: chain A residue  847 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  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  240 CYS
Chi-restraints excluded: chain B residue  326 PHE
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 2 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0000
   chunk 64 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0050
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS
** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.147390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.123657 restraints weight = 13273.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.127141 restraints weight = 6993.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129417 restraints weight = 4473.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6174  Z= 0.116
  Angle     :  0.631  12.897   8345  Z= 0.319
  Chirality :  0.040   0.164    926
  Planarity :  0.004   0.047   1071
  Dihedral  :  4.535  20.989    810
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.70 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.32), residues: 738
  helix:  0.20 (0.25), residues: 441
  sheet: -2.51 (1.77), residues: 10
  loop : -1.39 (0.40), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  43 
 HIS   0.008   0.001   HIS A 757 
 PHE   0.026   0.001   PHE B 326 
 TYR   0.017   0.001   TYR B   9 
 ARG   0.004   0.001   ARG A 726 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  249)
  hydrogen bonds       : angle       4.50994 (  741)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       1.87877 (    2)
  covalent geometry    : bond        0.00262 ( 6173)
  covalent geometry    : angle       0.63078 ( 8343)

*********************** 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
  145 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  689 HIS cc_start: 0.5307 (OUTLIER) cc_final: 0.4895 (t70)
REVERT: A  704 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8678 (mp)
REVERT: A  788 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8331 (mt-10)
REVERT: A  803 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7272 (tm-30)
REVERT: A  819 ASP cc_start: 0.7735 (m-30) cc_final: 0.7201 (t70)
REVERT: B  108 MET cc_start: 0.8551 (tpt) cc_final: 0.8236 (tmm)
REVERT: B  137 MET cc_start: 0.6480 (pmm) cc_final: 0.6048 (pmm)
REVERT: B  214 TYR cc_start: 0.7348 (t80) cc_final: 0.7011 (t80)
REVERT: B  250 MET cc_start: 0.8185 (tpp) cc_final: 0.7932 (tpp)
  outliers start: 21
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1581
  time to fit residues: 31.9093
Evaluate side-chains
  133 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  708 ILE
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  891 VAL
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  240 CYS
Chi-restraints excluded: chain B residue  258 VAL
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 7 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.146391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122866 restraints weight = 13588.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.126289 restraints weight = 7142.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.128567 restraints weight = 4586.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6174  Z= 0.134
  Angle     :  0.652  11.254   8345  Z= 0.330
  Chirality :  0.041   0.198    926
  Planarity :  0.004   0.044   1071
  Dihedral  :  4.560  21.862    810
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.69 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 23.93 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.32), residues: 738
  helix:  0.15 (0.25), residues: 442
  sheet: -2.50 (1.77), residues: 10
  loop : -1.43 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 166 
 HIS   0.007   0.001   HIS A 757 
 PHE   0.032   0.002   PHE B  91 
 TYR   0.023   0.001   TYR B 204 
 ARG   0.008   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  249)
  hydrogen bonds       : angle       4.59875 (  741)
  SS BOND              : bond        0.00268 (    1)
  SS BOND              : angle       1.98323 (    2)
  covalent geometry    : bond        0.00324 ( 6173)
  covalent geometry    : angle       0.65131 ( 8343)

********************** 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
  136 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  676 TYR cc_start: 0.6832 (t80) cc_final: 0.6621 (t80)
REVERT: A  689 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.4916 (t70)
REVERT: A  704 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8696 (mp)
REVERT: A  788 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8313 (mt-10)
REVERT: A  803 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7321 (tm-30)
REVERT: A  819 ASP cc_start: 0.7637 (m-30) cc_final: 0.7157 (t70)
REVERT: B  250 MET cc_start: 0.8164 (tpp) cc_final: 0.7940 (tpp)
  outliers start: 18
  outliers final: 14
  residues processed: 130
  average time/residue: 0.1429
  time to fit residues: 26.6382
Evaluate side-chains
  129 residues out of total 676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  813 LEU
Chi-restraints excluded: chain A residue  847 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  891 VAL
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  951 SER
Chi-restraints excluded: chain A residue  954 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  240 CYS
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 13 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.150234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.127061 restraints weight = 12730.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.130409 restraints weight = 6644.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.132620 restraints weight = 4250.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.5327

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= 0.141
  Angle     :  0.656  10.976   8345  Z= 0.331
  Chirality :  0.042   0.197    926
  Planarity :  0.004   0.043   1071
  Dihedral  :  4.566  23.034    810
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.64 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.85 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.32), residues: 738
  helix:  0.13 (0.25), residues: 442
  sheet: -2.65 (1.74), residues: 10
  loop : -1.37 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 166 
 HIS   0.007   0.001   HIS A 757 
 PHE   0.017   0.002   PHE B 326 
 TYR   0.022   0.002   TYR B 204 
 ARG   0.008   0.001   ARG B 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  249)
  hydrogen bonds       : angle       4.56054 (  741)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       1.74569 (    2)
  covalent geometry    : bond        0.00340 ( 6173)
  covalent geometry    : angle       0.65589 ( 8343)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2534.59 seconds
wall clock time: 46 minutes 48.88 seconds (2808.88 seconds total)