Starting phenix.real_space_refine
on Thu Mar 13 19:13:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d81_27242/03_2025/8d81_27242.cif"
  }
  resolution = 3.9
  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=  -0.001 sd=   0.042
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      56      5.16       5
     C    5883      2.51       5
     N    1563      2.21       5
     O    1745      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9248
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6290
          Classifications: {'peptide': 817}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 790}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 110
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 73
    Chain: "B"
      Number of atoms: 2937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2937
          Classifications: {'peptide': 381}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 20, 'TRANS': 360}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 21
          Unusual residues: {' ZN': 1, 'Y70': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8449  SG  CYS B 323      14.794  80.857  40.508  1.00  0.00           S
  ATOM   8465  SG  CYS B 326      11.359  81.448  42.109  1.00  0.00           S
  ATOM   8965  SG  CYS B 391      12.206  83.079  38.765  1.00  0.00           S
  ATOM   8984  SG  CYS B 394      13.753  84.339  41.887  1.00  0.00           S

  Time building chain proxies: 5.56, per 1000 atoms: 0.60
  Number of scatterers: 9248
  At special positions: 0
  Unit cell: (98.28, 114.66, 99.19, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      56     16.00
     O    1745      8.00
     N    1563      7.00
     C    5883      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.69
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 394 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 391 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 326 "
        pdb="ZN    ZN B 501 " - pdb=" SG  CYS B 323 "
      Number of angles added : 6


  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2244

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 22 sheets defined
      15.6% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 251 through 255
      removed outlier: 4.195A  pdb=" N   GLN A 255 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 381 through 384
    Processing helix  chain 'A' and resid 985 through 990
    Processing helix  chain 'A' and resid 1044 through 1059
      removed outlier: 3.736A  pdb=" N   ASN A1049 " --> pdb=" O   GLU A1045 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A1059 " --> pdb=" O   GLN A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1068
      removed outlier: 3.547A  pdb=" N   LYS A1067 " --> pdb=" O   SER A1064 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   ILE A1068 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1064 through 1068'
    Processing helix  chain 'A' and resid 1069 through 1075
    Processing helix  chain 'A' and resid 1091 through 1096
    Processing helix  chain 'A' and resid 1097 through 1100
    Processing helix  chain 'A' and resid 1101 through 1109
      removed outlier: 3.743A  pdb=" N   GLN A1106 " --> pdb=" O   ARG A1102 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLU A1107 " --> pdb=" O   PRO A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1138
      removed outlier: 3.661A  pdb=" N   ILE A1130 " --> pdb=" O   ALA A1126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 57
    Processing helix  chain 'B' and resid 58 through 61
    Processing helix  chain 'B' and resid 103 through 115
    Processing helix  chain 'B' and resid 220 through 232
      removed outlier: 3.701A  pdb=" N   GLN B 225 " --> pdb=" O   TYR B 221 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LYS B 226 " --> pdb=" O   LYS B 222 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 237
      removed outlier: 4.219A  pdb=" N   ASN B 236 " --> pdb=" O   HIS B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 248
      removed outlier: 3.880A  pdb=" N   TYR B 245 " --> pdb=" O   PRO B 241 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR B 248 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 265
    Processing helix  chain 'B' and resid 276 through 287
    Processing helix  chain 'B' and resid 291 through 301
    Processing helix  chain 'B' and resid 303 through 318
    Processing helix  chain 'B' and resid 329 through 333
      removed outlier: 3.618A  pdb=" N   THR B 332 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1004 through 1009
      removed outlier: 3.857A  pdb=" N   VAL A1006 " --> pdb=" O   GLY A1031 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   GLY A1026 " --> pdb=" O   SER A1042 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   SER A1042 " --> pdb=" O   GLY A1026 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A1038 " --> pdb=" O   PHE A1030 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ILE A1037 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   ASN A   4 " --> pdb=" O   ILE A1089 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21
      removed outlier: 3.633A  pdb=" N   GLY A  21 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A  30 " --> pdb=" O   GLY A  21 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR A  42 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS A  53 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   VAL A  43 " --> pdb=" O   PRO A  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 67
      removed outlier: 6.692A  pdb=" N   LEU A  80 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   MET A  64 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   PHE A  78 " --> pdb=" O   MET A  64 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LEU A  66 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU A  76 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   THR A  81 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN A  85 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   ALA A  86 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   HIS A 105 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ILE A  88 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS A  92 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP A  99 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124
    Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 169
      removed outlier: 6.855A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   HIS A 189 " --> pdb=" O   TYR A 182 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 221
      removed outlier: 3.524A  pdb=" N   MET A 218 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 240
      removed outlier: 3.589A  pdb=" N   ILE A 248 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 258 through 263
      removed outlier: 3.505A  pdb=" N   CYS A 260 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN A 262 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 272 " --> pdb=" O   ASN A 262 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 273 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASP A 275 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   ARG A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY A 306 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   MET A 282 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   LEU A 304 " --> pdb=" O   MET A 282 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   LEU A 284 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   VAL A 302 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 289 through 290
      removed outlier: 4.339A  pdb=" N   GLU A 289 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR A 296 " --> pdb=" O   GLU A 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 321 through 322
      removed outlier: 6.687A  pdb=" N   SER A 331 " --> pdb=" O   THR A 352 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   THR A 352 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   LEU A 333 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL A 348 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 362 through 365
      removed outlier: 3.641A  pdb=" N   ILE A 390 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG A 388 " --> pdb=" O   THR A 377 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 720 through 727
      removed outlier: 6.477A  pdb=" N   SER A 738 " --> pdb=" O   PRO A 721 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   LYS A 723 " --> pdb=" O   LEU A 736 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 736 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   CYS A 732 " --> pdb=" O   GLN A 727 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   HIS A 803 " --> pdb=" O   ILE A 793 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASP A 795 " --> pdb=" O   VAL A 801 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL A 801 " --> pdb=" O   ASP A 795 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 811 through 819
      removed outlier: 6.647A  pdb=" N   GLY A 832 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LEU A 816 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ILE A 830 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 4.951A  pdb=" N   SER A 818 " --> pdb=" O   TYR A 828 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   TYR A 828 " --> pdb=" O   SER A 818 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 870 through 876
      removed outlier: 4.836A  pdb=" N   SER A 872 " --> pdb=" O   SER A 883 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A 883 " --> pdb=" O   SER A 872 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL A 888 " --> pdb=" O   ASN A 904 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   ASN A 904 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LEU A 890 " --> pdb=" O   GLU A 902 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 914 through 917
      removed outlier: 3.575A  pdb=" N   LYS A 915 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU A 932 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 957 through 959
      removed outlier: 3.501A  pdb=" N   ASN A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   GLN A 978 " --> pdb=" O   GLU A 994 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   GLU A 994 " --> pdb=" O   GLN A 978 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 66
      removed outlier: 8.278A  pdb=" N   GLN B 134 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   LYS B 166 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   GLY B 136 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   ARG B 164 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR B 138 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR B 142 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   LYS B 158 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL B 157 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 79 through 82
      removed outlier: 3.645A  pdb=" N   ILE B  81 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA B 180 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   LYS B 158 " --> pdb=" O   TYR B 142 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR B 142 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   THR B 138 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   ARG B 164 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   GLY B 136 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   LYS B 166 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   GLN B 134 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   PHE B 135 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322
      removed outlier: 3.613A  pdb=" N   LEU B 423 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 348 through 351
      removed outlier: 4.318A  pdb=" N   ASN B 351 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
      removed outlier: 5.544A  pdb=" N   TYR B 355 " --> pdb=" O   ASN B 351 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362
      removed outlier: 3.533A  pdb=" N   VAL B 362 " --> pdb=" O   TRP B 415 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 368 through 370
      removed outlier: 4.475A  pdb=" N   ALA B 385 " --> pdb=" O   THR B 403 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.31

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1559
        1.31 -     1.44: 2435
        1.44 -     1.56: 5357
        1.56 -     1.69: 0
        1.69 -     1.82: 82
  Bond restraints: 9433
  Sorted by residual:
  bond pdb=" C15 Y70 B 502 "
       pdb=" N16 Y70 B 502 "
    ideal  model  delta    sigma   weight residual
    1.372  1.483 -0.111 2.00e-02 2.50e+03 3.10e+01
  bond pdb=" C6  Y70 B 502 "
       pdb=" N10 Y70 B 502 "
    ideal  model  delta    sigma   weight residual
    1.343  1.453 -0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" C17 Y70 B 502 "
       pdb=" N16 Y70 B 502 "
    ideal  model  delta    sigma   weight residual
    1.383  1.489 -0.106 2.00e-02 2.50e+03 2.80e+01
  bond pdb=" N   PRO A 825 "
       pdb=" CA  PRO A 825 "
    ideal  model  delta    sigma   weight residual
    1.469  1.530 -0.061 1.25e-02 6.40e+03 2.39e+01
  bond pdb=" C5  Y70 B 502 "
       pdb=" C9  Y70 B 502 "
    ideal  model  delta    sigma   weight residual
    1.459  1.542 -0.083 2.00e-02 2.50e+03 1.73e+01
  ... (remaining 9428 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 12542
        2.05 -     4.10: 239
        4.10 -     6.15: 26
        6.15 -     8.20: 7
        8.20 -    10.25: 2
  Bond angle restraints: 12816
  Sorted by residual:
  angle pdb=" N   PRO B  98 "
        pdb=" CA  PRO B  98 "
        pdb=" CB  PRO B  98 "
      ideal   model   delta    sigma   weight residual
     103.25  111.06   -7.81 1.05e+00 9.07e-01 5.53e+01
  angle pdb=" C   ASP A 824 "
        pdb=" N   PRO A 825 "
        pdb=" CA  PRO A 825 "
      ideal   model   delta    sigma   weight residual
     120.04  128.00   -7.96 1.08e+00 8.57e-01 5.43e+01
  angle pdb=" C   TRP A1073 "
        pdb=" N   ARG A1074 "
        pdb=" CA  ARG A1074 "
      ideal   model   delta    sigma   weight residual
     122.29  114.11    8.18 1.56e+00 4.11e-01 2.75e+01
  angle pdb=" C   THR A1125 "
        pdb=" CA  THR A1125 "
        pdb=" CB  THR A1125 "
      ideal   model   delta    sigma   weight residual
     115.79  110.12    5.67 1.19e+00 7.06e-01 2.27e+01
  angle pdb=" N   ASP A1116 "
        pdb=" CA  ASP A1116 "
        pdb=" C   ASP A1116 "
      ideal   model   delta    sigma   weight residual
     112.93  107.41    5.52 1.33e+00 5.65e-01 1.72e+01
  ... (remaining 12811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.92: 5293
       23.92 -    47.84: 316
       47.84 -    71.77: 22
       71.77 -    95.69: 15
       95.69 -   119.61: 3
  Dihedral angle restraints: 5649
    sinusoidal: 2170
      harmonic: 3479
  Sorted by residual:
  dihedral pdb=" CA  GLY B  69 "
           pdb=" C   GLY B  69 "
           pdb=" N   ARG B  70 "
           pdb=" CA  ARG B  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.20   27.80     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  VAL B  80 "
           pdb=" C   VAL B  80 "
           pdb=" N   ILE B  81 "
           pdb=" CA  ILE B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ILE B 152 "
           pdb=" C   ILE B 152 "
           pdb=" N   GLU B 153 "
           pdb=" CA  GLU B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.79   21.21     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 5646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1249
       0.064 -    0.127: 208
       0.127 -    0.191: 9
       0.191 -    0.254: 6
       0.254 -    0.318: 3
  Chirality restraints: 1475
  Sorted by residual:
  chirality pdb=" CA  VAL B 182 "
            pdb=" N   VAL B 182 "
            pdb=" C   VAL B 182 "
            pdb=" CB  VAL B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.76   -0.32 2.00e-01 2.50e+01 2.52e+00
  chirality pdb=" CA  CYS A 725 "
            pdb=" N   CYS A 725 "
            pdb=" C   CYS A 725 "
            pdb=" CB  CYS A 725 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  VAL B 182 "
            pdb=" CA  VAL B 182 "
            pdb=" CG1 VAL B 182 "
            pdb=" CG2 VAL B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.81e+00
  ... (remaining 1472 not shown)

  Planarity restraints: 1648
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 724 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   ILE A 724 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE A 724 "    0.015 2.00e-02 2.50e+03
        pdb=" N   CYS A 725 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 180 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   ALA B 180 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   ALA B 180 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS B 181 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1022 "    0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO A1023 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A1023 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1023 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1645 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2119
        2.79 -     3.32: 8307
        3.32 -     3.85: 14249
        3.85 -     4.37: 16062
        4.37 -     4.90: 28803
  Nonbonded interactions: 69540
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 351 "
            pdb=" O   TYR B 355 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OE1 GLU A 213 "
            pdb=" OG  SER A 236 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" N   ASN A 826 "
            pdb=" OD1 ASN A 826 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" ND2 ASN A  36 "
            pdb=" OD1 ASN A1034 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" OE2 GLU A  72 "
            pdb=" NH2 ARG A 103 "
     model   vdw
     2.329 3.120
  ... (remaining 69535 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:             0.700
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.500
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
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      :  0.004   0.111   9433  Z= 0.281
  Angle     :  0.654  10.247  12816  Z= 0.377
  Chirality :  0.049   0.318   1475
  Planarity :  0.004   0.048   1648
  Dihedral  : 14.939 119.609   3405
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  7.06 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  1.02 %
    Favored  : 97.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -2.23 (0.24), residues: 1190
  helix: -0.36 (0.42), residues: 164
  sheet: -1.30 (0.29), residues: 352
  loop : -1.89 (0.22), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 207 
 HIS   0.002   0.000   HIS B  73 
 PHE   0.010   0.001   PHE A1072 
 TYR   0.011   0.001   TYR A 828 
 ARG   0.003   0.000   ARG A 198 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A  135 LEU cc_start: 0.8929 (mt) cc_final: 0.8694 (mp)
REVERT: B   89 MET cc_start: 0.6768 (ptm) cc_final: 0.6307 (ptt)
REVERT: B  313 ASP cc_start: 0.7336 (t70) cc_final: 0.6954 (t0)
  outliers start: 13
  outliers final: 2
  residues processed: 168
  average time/residue: 0.1822
  time to fit residues: 44.3693
Evaluate side-chains
  121 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 ASN
Chi-restraints excluded: chain B residue   73 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   chunk 50 optimal weight:    0.2980
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 93 optimal weight:    9.9990
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.2980
   chunk 69 optimal weight:   10.0000
   chunk 108 optimal weight:    9.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 105 HIS
A 163 HIS
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.189525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.154034 restraints weight = 10536.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.152632 restraints weight = 14196.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.149832 restraints weight = 13991.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9433  Z= 0.273
  Angle     :  0.593   6.425  12816  Z= 0.308
  Chirality :  0.045   0.247   1475
  Planarity :  0.004   0.046   1648
  Dihedral  :  5.680  67.927   1302
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.55 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  9.75 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -2.02 (0.24), residues: 1190
  helix:  0.05 (0.42), residues: 169
  sheet: -1.29 (0.27), residues: 375
  loop : -1.74 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 207 
 HIS   0.003   0.001   HIS A 805 
 PHE   0.029   0.002   PHE B 120 
 TYR   0.013   0.001   TYR A  91 
 ARG   0.003   0.000   ARG B 283 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 1.150 
Fit side-chains
REVERT: B   89 MET cc_start: 0.8001 (ptm) cc_final: 0.7515 (ptt)
REVERT: B  357 HIS cc_start: 0.6994 (t-90) cc_final: 0.6782 (t-90)
  outliers start: 12
  outliers final: 10
  residues processed: 129
  average time/residue: 0.2065
  time to fit residues: 39.1004
Evaluate side-chains
  123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 55 optimal weight:    0.3980
   chunk 61 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0000
   chunk 15 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0470
   overall best weight:    0.8484

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 ASN
A 789 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.194591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152956 restraints weight = 10765.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150505 restraints weight = 17539.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.151560 restraints weight = 14905.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9433  Z= 0.182
  Angle     :  0.526   8.457  12816  Z= 0.273
  Chirality :  0.044   0.179   1475
  Planarity :  0.004   0.045   1648
  Dihedral  :  4.530  47.360   1300
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.05 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.79 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.82 (0.24), residues: 1190
  helix:  0.16 (0.42), residues: 172
  sheet: -1.21 (0.27), residues: 370
  loop : -1.58 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.003   0.001   HIS B  73 
 PHE   0.028   0.001   PHE B 120 
 TYR   0.011   0.001   TYR A  91 
 ARG   0.006   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 2.722 
Fit side-chains
REVERT: A  137 ASP cc_start: 0.7727 (m-30) cc_final: 0.7523 (p0)
REVERT: B   64 MET cc_start: 0.3634 (mmm) cc_final: 0.3240 (mmm)
REVERT: B   89 MET cc_start: 0.8152 (ptm) cc_final: 0.7729 (ptt)
REVERT: B  331 ILE cc_start: 0.7232 (pt) cc_final: 0.6935 (mm)
  outliers start: 13
  outliers final: 9
  residues processed: 144
  average time/residue: 0.2967
  time to fit residues: 62.9728
Evaluate side-chains
  128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0030
   chunk 111 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0770
   chunk 26 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.1350

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.192816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.150411 restraints weight = 10671.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.148343 restraints weight = 18097.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.149163 restraints weight = 13567.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9433  Z= 0.206
  Angle     :  0.530   7.172  12816  Z= 0.276
  Chirality :  0.044   0.210   1475
  Planarity :  0.003   0.046   1648
  Dihedral  :  4.425  48.683   1300
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.72 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.71 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.70 (0.24), residues: 1190
  helix:  0.29 (0.43), residues: 172
  sheet: -1.08 (0.27), residues: 362
  loop : -1.55 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 207 
 HIS   0.002   0.001   HIS A 789 
 PHE   0.031   0.001   PHE B 120 
 TYR   0.011   0.001   TYR A  91 
 ARG   0.005   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.8704 (mttt) cc_final: 0.8054 (mttp)
REVERT: A  207 TRP cc_start: 0.8567 (OUTLIER) cc_final: 0.6287 (p-90)
REVERT: B   64 MET cc_start: 0.3635 (mmm) cc_final: 0.3152 (mmm)
REVERT: B   89 MET cc_start: 0.8218 (ptm) cc_final: 0.7812 (ptt)
  outliers start: 20
  outliers final: 11
  residues processed: 142
  average time/residue: 0.2479
  time to fit residues: 52.4139
Evaluate side-chains
  129 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  357 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 113 optimal weight:   20.0000
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 GLN
B 103 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.183654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146102 restraints weight = 10690.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.144024 restraints weight = 18558.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.142944 restraints weight = 17142.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9433  Z= 0.435
  Angle     :  0.649  12.660  12816  Z= 0.335
  Chirality :  0.046   0.196   1475
  Planarity :  0.004   0.049   1648
  Dihedral  :  4.920  52.032   1300
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  7.90 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.21 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.89 (0.24), residues: 1190
  helix:  0.11 (0.42), residues: 171
  sheet: -1.20 (0.27), residues: 357
  loop : -1.66 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A1070 
 PHE   0.031   0.002   PHE B 120 
 TYR   0.020   0.002   TYR A  91 
 ARG   0.004   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8793 (OUTLIER) cc_final: 0.6798 (p-90)
REVERT: A 1128 ASP cc_start: 0.6953 (m-30) cc_final: 0.6676 (m-30)
REVERT: B   89 MET cc_start: 0.8272 (ptm) cc_final: 0.7860 (ptt)
  outliers start: 27
  outliers final: 19
  residues processed: 140
  average time/residue: 0.2118
  time to fit residues: 43.2628
Evaluate side-chains
  136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 THR
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 106 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 113 optimal weight:   20.0000
   chunk 78 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0170
   chunk 100 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0770
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.191881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.149583 restraints weight = 10649.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.147264 restraints weight = 18110.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.148044 restraints weight = 16250.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9433  Z= 0.170
  Angle     :  0.551  12.282  12816  Z= 0.277
  Chirality :  0.043   0.163   1475
  Planarity :  0.003   0.046   1648
  Dihedral  :  4.503  51.653   1300
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  5.80 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.33 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.72 (0.24), residues: 1190
  helix:  0.11 (0.42), residues: 174
  sheet: -1.16 (0.27), residues: 375
  loop : -1.46 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.002   0.000   HIS A 261 
 PHE   0.031   0.001   PHE B 120 
 TYR   0.010   0.001   TYR A  91 
 ARG   0.005   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 1.011 
Fit side-chains
REVERT: A  207 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.6228 (p-90)
REVERT: A 1105 MET cc_start: 0.7674 (mtt) cc_final: 0.7369 (mtt)
REVERT: B   89 MET cc_start: 0.8478 (ptm) cc_final: 0.8072 (ptt)
REVERT: B  111 ARG cc_start: 0.8211 (ptt-90) cc_final: 0.7899 (ptt-90)
REVERT: B  336 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4430 (tm-30)
  outliers start: 22
  outliers final: 14
  residues processed: 136
  average time/residue: 0.1833
  time to fit residues: 36.8816
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  336 GLU
Chi-restraints excluded: chain B residue  357 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:    0.8980
   chunk 90 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0050
   chunk 78 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1070 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.190033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.146907 restraints weight = 10546.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.138158 restraints weight = 11413.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.140641 restraints weight = 12286.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9433  Z= 0.169
  Angle     :  0.536  10.696  12816  Z= 0.271
  Chirality :  0.043   0.146   1475
  Planarity :  0.003   0.046   1648
  Dihedral  :  4.347  52.335   1300
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.47 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.84 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.57 (0.24), residues: 1190
  helix:  0.18 (0.42), residues: 174
  sheet: -1.00 (0.27), residues: 372
  loop : -1.39 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 207 
 HIS   0.002   0.000   HIS A 805 
 PHE   0.034   0.001   PHE B 120 
 TYR   0.009   0.001   TYR A  91 
 ARG   0.004   0.000   ARG A1138 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A  207 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.6246 (p-90)
REVERT: A 1105 MET cc_start: 0.7713 (mtt) cc_final: 0.7491 (mtt)
REVERT: B   89 MET cc_start: 0.8542 (ptm) cc_final: 0.8144 (ptt)
REVERT: B  111 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.8020 (ptt-90)
REVERT: B  338 PHE cc_start: 0.4745 (m-80) cc_final: 0.4458 (m-80)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1817
  time to fit residues: 34.7993
Evaluate side-chains
  135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  357 HIS
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 87 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 GLN
A 789 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.187497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.149654 restraints weight = 10664.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.147919 restraints weight = 18048.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148432 restraints weight = 16306.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9433  Z= 0.224
  Angle     :  0.544  10.201  12816  Z= 0.277
  Chirality :  0.043   0.138   1475
  Planarity :  0.003   0.047   1648
  Dihedral  :  4.439  54.000   1300
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.81 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.65 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.61 (0.24), residues: 1190
  helix:  0.20 (0.42), residues: 173
  sheet: -1.04 (0.27), residues: 376
  loop : -1.42 (0.24), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.008   0.001   HIS A 789 
 PHE   0.031   0.001   PHE B 120 
 TYR   0.016   0.001   TYR B 363 
 ARG   0.002   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8780 (mttt) cc_final: 0.8112 (mttp)
REVERT: A  207 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.6390 (p-90)
REVERT: B   89 MET cc_start: 0.8160 (ptm) cc_final: 0.7787 (ptt)
REVERT: B  251 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7967 (tp30)
REVERT: B  336 GLU cc_start: 0.3862 (tm-30) cc_final: 0.3647 (tt0)
  outliers start: 24
  outliers final: 20
  residues processed: 137
  average time/residue: 0.1973
  time to fit residues: 39.7263
Evaluate side-chains
  133 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  731 GLN
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  954 MET
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  357 HIS
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 115 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 118 optimal weight:   10.0000
   chunk 79 optimal weight:    8.9990
   chunk 97 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0670
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.191925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.154268 restraints weight = 10508.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.152645 restraints weight = 17702.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.151074 restraints weight = 15929.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9433  Z= 0.159
  Angle     :  0.539   9.786  12816  Z= 0.275
  Chirality :  0.043   0.136   1475
  Planarity :  0.003   0.046   1648
  Dihedral  :  4.328  53.760   1300
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.22 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.77 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.51 (0.24), residues: 1190
  helix:  0.38 (0.43), residues: 168
  sheet: -0.94 (0.28), residues: 361
  loop : -1.39 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 207 
 HIS   0.009   0.001   HIS A 789 
 PHE   0.032   0.001   PHE B 120 
 TYR   0.025   0.001   TYR B 363 
 ARG   0.003   0.000   ARG A1138 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5934 (mmm) cc_final: 0.5521 (mmm)
REVERT: A  207 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.6244 (p-90)
REVERT: B   89 MET cc_start: 0.8260 (ptm) cc_final: 0.7888 (ptt)
  outliers start: 17
  outliers final: 14
  residues processed: 124
  average time/residue: 0.1909
  time to fit residues: 34.8738
Evaluate side-chains
  131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  954 MET
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  357 HIS
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:   30.0000
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 104 optimal weight:    0.3980
   chunk 96 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.191226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.151383 restraints weight = 10938.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.148677 restraints weight = 18612.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.145404 restraints weight = 16726.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9433  Z= 0.250
  Angle     :  0.565   9.690  12816  Z= 0.288
  Chirality :  0.044   0.134   1475
  Planarity :  0.003   0.048   1648
  Dihedral  :  4.462  55.246   1300
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.89 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.07 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.58 (0.24), residues: 1190
  helix:  0.22 (0.42), residues: 173
  sheet: -1.04 (0.27), residues: 373
  loop : -1.39 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.008   0.001   HIS A 789 
 PHE   0.031   0.001   PHE B 120 
 TYR   0.013   0.001   TYR B 363 
 ARG   0.002   0.000   ARG B 111 

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

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

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2380 Ramachandran restraints generated.
    1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6173 (mmm) cc_final: 0.5792 (mmm)
REVERT: A  207 TRP cc_start: 0.8655 (OUTLIER) cc_final: 0.6311 (p-90)
REVERT: A 1128 ASP cc_start: 0.7278 (m-30) cc_final: 0.6809 (m-30)
REVERT: B   89 MET cc_start: 0.8587 (ptm) cc_final: 0.8247 (ptt)
REVERT: B  251 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8230 (tp30)
REVERT: B  336 GLU cc_start: 0.4811 (tm-30) cc_final: 0.4505 (tt0)
  outliers start: 20
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1969
  time to fit residues: 38.3002
Evaluate side-chains
  126 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  732 CYS
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue 1004 VAL
Chi-restraints excluded: chain B residue   73 HIS
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  357 HIS
Chi-restraints excluded: chain B residue  358 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 34 optimal weight:    0.2980
   chunk 11 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 91 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.189788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.148547 restraints weight = 10638.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.142625 restraints weight = 17038.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.145162 restraints weight = 14220.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9433  Z= 0.214
  Angle     :  0.577  10.480  12816  Z= 0.291
  Chirality :  0.043   0.139   1475
  Planarity :  0.003   0.047   1648
  Dihedral  :  4.434  55.142   1300
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  6.72 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 18.78 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.58 (0.24), residues: 1190
  helix:  0.17 (0.41), residues: 173
  sheet: -1.01 (0.27), residues: 373
  loop : -1.39 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 207 
 HIS   0.008   0.001   HIS A 789 
 PHE   0.032   0.001   PHE B 120 
 TYR   0.015   0.001   TYR B 363 
 ARG   0.002   0.000   ARG B 111 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2850.67 seconds
wall clock time: 53 minutes 0.64 seconds (3180.64 seconds total)