Starting phenix.real_space_refine
on Tue Jul 29 22:55:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f9z_31501/07_2025/7f9z_31501_neut.cif"
  }
  resolution = 3.2
  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=   0.003 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2189 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    6350      2.51       5
     N    1715      2.21       5
     O    1853      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9982
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1877
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 64
          Unusual residues: {'NH2': 1}
          Classifications: {'peptide': 6, 'undetermined': 1}
          Modifications used: {'PEPT-D': 6}
          Link IDs: {'CIS': 3, 'NH2_CTERM': 1, 'TRANS': 2}
    Chain: "E"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1777
          Classifications: {'peptide': 231}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 973
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 973
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "R"
      Number of atoms: 2255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2255
          Classifications: {'peptide': 282}
          Link IDs: {'PTRANS': 11, 'TRANS': 270}
          Chain breaks: 1
  Time building chain proxies: 6.08, per 1000 atoms: 0.61
  Number of scatterers: 9982
  At special positions: 0
  Unit cell: (111.815, 114.95, 122.265, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1853      8.00
     N    1715      7.00
     C    6350      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.04
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DHI C   1 "
        pdb=" CB  DTR C   2 "
        pdb=" CB  DAL C   3 "
        pdb=" CB  DTR C   4 "
        pdb=" CB  DPN C   5 "
        pdb=" CB  DLY C   6 "
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 15 sheets defined
      35.9% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.837A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.586A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.083A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.312A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.690A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'E' and resid 62 through 65
      removed outlier: 3.809A  pdb=" N   LYS E  65 " --> pdb=" O   ASP E  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 62 through 65'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.023A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.684A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.508A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 40 through 69
      removed outlier: 3.618A  pdb=" N   ALA R  59 " --> pdb=" O   VAL R  55 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   VAL R  68 " --> pdb=" O   THR R  64 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   SER R  69 " --> pdb=" O   MET R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 71 through 75
      removed outlier: 3.685A  pdb=" N   LEU R  74 " --> pdb=" O   PHE R  71 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 76 through 94
    Processing helix  chain 'R' and resid 95 through 100
    Processing helix  chain 'R' and resid 100 through 105
    Processing helix  chain 'R' and resid 112 through 147
    Processing helix  chain 'R' and resid 151 through 155
      removed outlier: 3.690A  pdb=" N   VAL R 155 " --> pdb=" O   LYS R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 156 through 175
    Processing helix  chain 'R' and resid 176 through 179
    Processing helix  chain 'R' and resid 201 through 207
      removed outlier: 3.617A  pdb=" N   VAL R 205 " --> pdb=" O   THR R 201 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 208 through 241
      removed outlier: 3.997A  pdb=" N   VAL R 212 " --> pdb=" O   GLY R 208 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER R 217 " --> pdb=" O   MET R 213 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
    Processing helix  chain 'R' and resid 258 through 290
      Proline residue:  R 278  - end of helix
      removed outlier: 4.091A  pdb=" N   ARG R 283 " --> pdb=" O   PHE R 279 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   PHE R 290 " --> pdb=" O   PHE R 286 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 294 through 323
      removed outlier: 4.154A  pdb=" N   ALA R 298 " --> pdb=" O   SER R 294 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
      removed outlier: 3.565A  pdb=" N   TYR R 323 " --> pdb=" O   ASN R 319 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 327 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.534A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.400A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.531A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.560A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.354A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN B 125 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.827A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.763A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.855A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.552A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.601A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL E   5 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   THR E  78 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ASP E  73 " --> pdb=" O   THR E  78 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR E  69 " --> pdb=" O   GLN E  82 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.757A  pdb=" N   THR E 115 " --> pdb=" O   TYR E  94 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR E  94 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E  92 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 142
      removed outlier: 3.642A  pdb=" N   THR E 141 " --> pdb=" O   ARG E 160 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.526A  pdb=" N   GLU E 246 " --> pdb=" O   VAL E 147 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.724A  pdb=" N   GLN N   5 " --> pdb=" O   ALA N  23 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.545A  pdb=" N   GLY N  10 " --> pdb=" O   GLN N 123 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 182 through 185

    480 hydrogen bonds defined for protein.
    1323 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: 3.19

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1607
        1.30 -     1.43: 2753
        1.43 -     1.56: 5745
        1.56 -     1.69: 2
        1.69 -     1.82: 91
  Bond restraints: 10198
  Sorted by residual:
  bond pdb=" C   DTR C   2 "
       pdb=" N   DAL C   3 "
    ideal  model  delta    sigma   weight residual
    1.329  1.509 -0.180 1.40e-02 5.10e+03 1.65e+02
  bond pdb=" C   DHI C   1 "
       pdb=" N   DTR C   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.499 -0.170 1.40e-02 5.10e+03 1.47e+02
  bond pdb=" C   DAL C   3 "
       pdb=" N   DTR C   4 "
    ideal  model  delta    sigma   weight residual
    1.329  1.480 -0.151 1.40e-02 5.10e+03 1.16e+02
  bond pdb=" C   DTR C   4 "
       pdb=" N   DPN C   5 "
    ideal  model  delta    sigma   weight residual
    1.329  1.476 -0.147 1.40e-02 5.10e+03 1.10e+02
  bond pdb=" C   DPN C   5 "
       pdb=" N   DLY C   6 "
    ideal  model  delta    sigma   weight residual
    1.329  1.474 -0.145 1.40e-02 5.10e+03 1.07e+02
  ... (remaining 10193 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 13631
        1.93 -     3.87: 150
        3.87 -     5.80: 30
        5.80 -     7.74: 4
        7.74 -     9.67: 3
  Bond angle restraints: 13818
  Sorted by residual:
  angle pdb=" CA  DPN C   5 "
        pdb=" C   DPN C   5 "
        pdb=" N   DLY C   6 "
      ideal   model   delta    sigma   weight residual
     116.20  125.87   -9.67 2.00e+00 2.50e-01 2.34e+01
  angle pdb=" CA  DTR C   2 "
        pdb=" C   DTR C   2 "
        pdb=" N   DAL C   3 "
      ideal   model   delta    sigma   weight residual
     116.20  125.11   -8.91 2.00e+00 2.50e-01 1.99e+01
  angle pdb=" CB  DHI C   1 "
        pdb=" CG  DHI C   1 "
        pdb=" CD2 DHI C   1 "
      ideal   model   delta    sigma   weight residual
     131.20  126.31    4.89 1.30e+00 5.92e-01 1.41e+01
  angle pdb=" O   DPN C   5 "
        pdb=" C   DPN C   5 "
        pdb=" N   DLY C   6 "
      ideal   model   delta    sigma   weight residual
     123.00  117.19    5.81 1.60e+00 3.91e-01 1.32e+01
  angle pdb=" O   DTR C   2 "
        pdb=" C   DTR C   2 "
        pdb=" N   DAL C   3 "
      ideal   model   delta    sigma   weight residual
     123.00  117.48    5.52 1.60e+00 3.91e-01 1.19e+01
  ... (remaining 13813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 5482
       17.63 -    35.26: 450
       35.26 -    52.89: 75
       52.89 -    70.52: 13
       70.52 -    88.16: 7
  Dihedral angle restraints: 6027
    sinusoidal: 2362
      harmonic: 3665
  Sorted by residual:
  dihedral pdb=" CA  LEU R  66 "
           pdb=" C   LEU R  66 "
           pdb=" N   VAL R  67 "
           pdb=" CA  VAL R  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.83   24.17     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CB  CYS R 116 "
           pdb=" SG  CYS R 116 "
           pdb=" SG  CYS R 198 "
           pdb=" CB  CYS R 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.01   39.01     1      1.00e+01 1.00e-02 2.14e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 6024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1477
       0.092 -    0.184: 73
       0.184 -    0.277: 0
       0.277 -    0.369: 1
       0.369 -    0.461: 2
  Chirality restraints: 1553
  Sorted by residual:
  chirality pdb=" CA  DPN C   5 "
            pdb=" N   DPN C   5 "
            pdb=" C   DPN C   5 "
            pdb=" CB  DPN C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.05   -0.46 2.00e-01 2.50e+01 5.32e+00
  chirality pdb=" CA  DLY C   6 "
            pdb=" N   DLY C   6 "
            pdb=" C   DLY C   6 "
            pdb=" CB  DLY C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.10   -0.41 2.00e-01 2.50e+01 4.20e+00
  chirality pdb=" CA  DTR C   4 "
            pdb=" N   DTR C   4 "
            pdb=" C   DTR C   4 "
            pdb=" CB  DTR C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.19   -0.32 2.00e-01 2.50e+01 2.53e+00
  ... (remaining 1550 not shown)

  Planarity restraints: 1753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS N  87 "   -0.033 5.00e-02 4.00e+02   5.01e-02 4.01e+00
        pdb=" N   PRO N  88 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO N  88 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO N  88 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 199 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO R 200 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO R 200 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO R 200 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR E 150 "    0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO E 151 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO E 151 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E 151 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1750 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 647
        2.74 -     3.28: 10195
        3.28 -     3.82: 16937
        3.82 -     4.36: 19815
        4.36 -     4.90: 34461
  Nonbonded interactions: 82055
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ILE E 100 "
            pdb=" OG  SER E 105 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASP A 331 "
            pdb=" NH1 ARG A 333 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   ILE E 138 "
            pdb=" OG1 THR E 238 "
     model   vdw
     2.266 3.040
  ... (remaining 82050 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 individual isotropic
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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.580
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.436  10201  Z= 0.536
  Angle     :  0.561   9.672  13822  Z= 0.324
  Chirality :  0.044   0.461   1553
  Planarity :  0.004   0.050   1753
  Dihedral  : 13.178  88.155   3661
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    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: 1244
  helix:  2.03 (0.26), residues: 395
  sheet:  1.14 (0.29), residues: 314
  loop :  0.20 (0.28), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.022   0.001   PHE R 119 
 TYR   0.013   0.001   TYR A 311 
 ARG   0.012   0.000   ARG B   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19522 (  480)
  hydrogen bonds       : angle       6.53407 ( 1323)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.75208 (    4)
  covalent geometry    : bond        0.00482 (10198)
  covalent geometry    : angle       0.56126 (13818)
  Misc. bond           : bond        0.43606 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 SER cc_start: 0.6231 (m) cc_final: 0.5993 (m)
REVERT: A  266 LEU cc_start: 0.8007 (tp) cc_final: 0.7622 (tp)
REVERT: A  272 ASP cc_start: 0.6629 (m-30) cc_final: 0.6303 (m-30)
REVERT: A  289 LEU cc_start: 0.7925 (mp) cc_final: 0.7721 (mp)
REVERT: B   61 MET cc_start: 0.6545 (ppp) cc_final: 0.6302 (ppp)
REVERT: B  170 ASP cc_start: 0.6958 (t70) cc_final: 0.6514 (t70)
REVERT: B  173 THR cc_start: 0.7586 (p) cc_final: 0.7283 (p)
REVERT: B  186 ASP cc_start: 0.6212 (m-30) cc_final: 0.5849 (m-30)
REVERT: B  190 LEU cc_start: 0.7915 (pp) cc_final: 0.7667 (pp)
REVERT: B  311 HIS cc_start: 0.7106 (m-70) cc_final: 0.6428 (m-70)
REVERT: E  172 THR cc_start: 0.8448 (p) cc_final: 0.8192 (p)
REVERT: E  190 TYR cc_start: 0.7535 (p90) cc_final: 0.7333 (p90)
REVERT: N   84 ASN cc_start: 0.7663 (m110) cc_final: 0.7424 (m110)
REVERT: R  137 LEU cc_start: 0.7003 (mt) cc_final: 0.6723 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2187
  time to fit residues: 73.3583
Evaluate side-chains
  219 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 93 optimal weight:    0.1980
   chunk 51 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 295 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.161550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143378 restraints weight = 13858.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3834 rms_B_bonded: 2.23
r_work: 0.3718 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10201  Z= 0.148
  Angle     :  0.552  10.108  13822  Z= 0.291
  Chirality :  0.044   0.464   1553
  Planarity :  0.005   0.048   1753
  Dihedral  :  4.462  56.449   1393
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  9.12 %
    Favored  : 89.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    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:  1.38 (0.24), residues: 1244
  helix:  1.88 (0.26), residues: 409
  sheet:  0.93 (0.28), residues: 337
  loop :  0.20 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.005   0.002   HIS B 142 
 PHE   0.020   0.002   PHE R 286 
 TYR   0.012   0.001   TYR N  94 
 ARG   0.006   0.001   ARG A 342 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  480)
  hydrogen bonds       : angle       4.60954 ( 1323)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.62961 (    4)
  covalent geometry    : bond        0.00332 (10198)
  covalent geometry    : angle       0.55148 (13818)
  Misc. bond           : bond        0.00141 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 262
  time to evaluate  : 1.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8097 (mmpt) cc_final: 0.7748 (mmpt)
REVERT: A  250 SER cc_start: 0.6336 (m) cc_final: 0.6080 (m)
REVERT: A  266 LEU cc_start: 0.8193 (tp) cc_final: 0.7850 (tp)
REVERT: A  293 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7518 (mtmt)
REVERT: A  347 ASP cc_start: 0.6867 (m-30) cc_final: 0.6663 (m-30)
REVERT: A  374 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7658 (mtm-85)
REVERT: A  381 ASP cc_start: 0.7950 (t0) cc_final: 0.7715 (t0)
REVERT: B   61 MET cc_start: 0.7609 (ppp) cc_final: 0.7366 (ppp)
REVERT: B  170 ASP cc_start: 0.7742 (t70) cc_final: 0.7207 (t70)
REVERT: B  196 THR cc_start: 0.8248 (m) cc_final: 0.7581 (p)
REVERT: B  220 GLN cc_start: 0.7837 (mt0) cc_final: 0.7614 (mt0)
REVERT: E  190 TYR cc_start: 0.7810 (p90) cc_final: 0.7404 (p90)
REVERT: N   83 MET cc_start: 0.7892 (mtt) cc_final: 0.7560 (mtt)
REVERT: N   84 ASN cc_start: 0.7888 (m110) cc_final: 0.7672 (m110)
REVERT: R   54 PHE cc_start: 0.7763 (t80) cc_final: 0.7500 (t80)
REVERT: R   93 PHE cc_start: 0.6097 (m-10) cc_final: 0.5820 (m-10)
  outliers start: 18
  outliers final: 11
  residues processed: 270
  average time/residue: 0.2727
  time to fit residues: 102.1265
Evaluate side-chains
  252 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 241
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  301 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 108 optimal weight:    0.8980
   chunk 119 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 220 GLN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.149702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131256 restraints weight = 14259.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.21
r_work: 0.3597 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  10201  Z= 0.217
  Angle     :  0.605   9.322  13822  Z= 0.322
  Chirality :  0.047   0.451   1553
  Planarity :  0.005   0.053   1753
  Dihedral  :  4.925  54.561   1393
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.18 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    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:  1.02 (0.24), residues: 1244
  helix:  1.53 (0.25), residues: 404
  sheet:  0.63 (0.28), residues: 341
  loop :  0.13 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E  36 
 HIS   0.009   0.002   HIS B 142 
 PHE   0.022   0.002   PHE R 286 
 TYR   0.015   0.002   TYR N  95 
 ARG   0.006   0.001   ARG R 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  480)
  hydrogen bonds       : angle       4.69295 ( 1323)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       1.14211 (    4)
  covalent geometry    : bond        0.00483 (10198)
  covalent geometry    : angle       0.60521 (13818)
  Misc. bond           : bond        0.00214 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 254
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8253 (tp) cc_final: 0.7966 (tp)
REVERT: A  293 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7683 (mtmt)
REVERT: A  343 LYS cc_start: 0.7667 (tttp) cc_final: 0.7033 (tttp)
REVERT: A  347 ASP cc_start: 0.7190 (m-30) cc_final: 0.6856 (m-30)
REVERT: A  370 GLU cc_start: 0.7619 (pm20) cc_final: 0.7275 (pm20)
REVERT: A  374 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7734 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8073 (t0) cc_final: 0.7636 (t0)
REVERT: B  135 VAL cc_start: 0.7917 (t) cc_final: 0.7659 (p)
REVERT: B  170 ASP cc_start: 0.7842 (t70) cc_final: 0.7523 (t70)
REVERT: E  190 TYR cc_start: 0.7987 (p90) cc_final: 0.7530 (p90)
REVERT: N   32 TYR cc_start: 0.8501 (m-80) cc_final: 0.8021 (m-80)
REVERT: N   84 ASN cc_start: 0.7872 (m110) cc_final: 0.7660 (m110)
REVERT: R   54 PHE cc_start: 0.7745 (t80) cc_final: 0.7465 (t80)
  outliers start: 25
  outliers final: 21
  residues processed: 266
  average time/residue: 0.2364
  time to fit residues: 85.3506
Evaluate side-chains
  258 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 237
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   18 ILE
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue   88 SER
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  301 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 118 optimal weight:    0.1980
   chunk 107 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 220 GLN
B 239 ASN
N  31 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.152707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.134631 restraints weight = 14106.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.25
r_work: 0.3603 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10201  Z= 0.124
  Angle     :  0.533   8.515  13822  Z= 0.278
  Chirality :  0.043   0.342   1553
  Planarity :  0.004   0.050   1753
  Dihedral  :  4.521  40.705   1393
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.48 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    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:  1.09 (0.24), residues: 1244
  helix:  1.69 (0.26), residues: 408
  sheet:  0.60 (0.29), residues: 330
  loop :  0.13 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.007   0.002   HIS A 220 
 PHE   0.022   0.002   PHE R 279 
 TYR   0.012   0.001   TYR R 313 
 ARG   0.008   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  480)
  hydrogen bonds       : angle       4.39520 ( 1323)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       0.67441 (    4)
  covalent geometry    : bond        0.00277 (10198)
  covalent geometry    : angle       0.53264 (13818)
  Misc. bond           : bond        0.00117 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 240
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 LEU cc_start: 0.8289 (tp) cc_final: 0.7979 (tp)
REVERT: A  336 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7122 (ttp80)
REVERT: A  347 ASP cc_start: 0.7117 (m-30) cc_final: 0.6844 (m-30)
REVERT: A  370 GLU cc_start: 0.7644 (pm20) cc_final: 0.7270 (pm20)
REVERT: A  374 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7748 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8010 (t0) cc_final: 0.7527 (t0)
REVERT: B   76 ASP cc_start: 0.7353 (p0) cc_final: 0.7143 (p0)
REVERT: B  170 ASP cc_start: 0.7899 (t70) cc_final: 0.7560 (t70)
REVERT: B  239 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7288 (t0)
REVERT: B  311 HIS cc_start: 0.7640 (m-70) cc_final: 0.6984 (m-70)
REVERT: B  333 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7156 (p0)
REVERT: E  190 TYR cc_start: 0.8013 (p90) cc_final: 0.7628 (p90)
REVERT: N   34 MET cc_start: 0.8003 (mmm) cc_final: 0.7446 (mmm)
REVERT: N   94 TYR cc_start: 0.8042 (m-80) cc_final: 0.7671 (m-80)
REVERT: R   54 PHE cc_start: 0.7683 (t80) cc_final: 0.7439 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 253
  average time/residue: 0.2536
  time to fit residues: 87.4604
Evaluate side-chains
  258 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 236
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  333 ASP
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  274 LEU
Chi-restraints excluded: chain R residue  301 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    0.4980
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 117 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 120 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 239 ASN
N  84 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.148359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130438 restraints weight = 13910.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 2.08
r_work: 0.3566 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10201  Z= 0.190
  Angle     :  0.572   8.165  13822  Z= 0.299
  Chirality :  0.045   0.278   1553
  Planarity :  0.005   0.052   1753
  Dihedral  :  4.662  33.037   1393
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.22 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1244
  helix:  1.52 (0.25), residues: 408
  sheet:  0.38 (0.29), residues: 335
  loop :  0.03 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  36 
 HIS   0.009   0.002   HIS A 220 
 PHE   0.020   0.002   PHE R 279 
 TYR   0.014   0.002   TYR N  95 
 ARG   0.008   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  480)
  hydrogen bonds       : angle       4.50311 ( 1323)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.70399 (    4)
  covalent geometry    : bond        0.00429 (10198)
  covalent geometry    : angle       0.57157 (13818)
  Misc. bond           : bond        0.00098 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 255
  time to evaluate  : 1.165 
Fit side-chains
REVERT: A  266 LEU cc_start: 0.8331 (tp) cc_final: 0.8028 (tp)
REVERT: A  293 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7654 (mtmt)
REVERT: A  347 ASP cc_start: 0.7134 (m-30) cc_final: 0.6841 (m-30)
REVERT: A  370 GLU cc_start: 0.7624 (pm20) cc_final: 0.7255 (pm20)
REVERT: A  374 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7845 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8089 (t0) cc_final: 0.7603 (t0)
REVERT: A  391 TYR cc_start: 0.7883 (m-10) cc_final: 0.7589 (m-10)
REVERT: B   78 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8086 (mttp)
REVERT: B  135 VAL cc_start: 0.7864 (t) cc_final: 0.7565 (p)
REVERT: B  170 ASP cc_start: 0.7865 (t70) cc_final: 0.7592 (t70)
REVERT: B  239 ASN cc_start: 0.8011 (t0) cc_final: 0.7612 (t0)
REVERT: B  311 HIS cc_start: 0.7656 (m-70) cc_final: 0.7251 (m-70)
REVERT: B  333 ASP cc_start: 0.7773 (p0) cc_final: 0.7497 (p0)
REVERT: E  190 TYR cc_start: 0.7957 (p90) cc_final: 0.7617 (p90)
REVERT: N   94 TYR cc_start: 0.8203 (m-80) cc_final: 0.7926 (m-80)
REVERT: R   54 PHE cc_start: 0.7595 (t80) cc_final: 0.7372 (t80)
  outliers start: 30
  outliers final: 21
  residues processed: 270
  average time/residue: 0.2824
  time to fit residues: 106.6336
Evaluate side-chains
  270 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 249
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  250 SER
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  310 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.146693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128943 restraints weight = 14010.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.07
r_work: 0.3551 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  10201  Z= 0.225
  Angle     :  0.597   7.538  13822  Z= 0.314
  Chirality :  0.046   0.247   1553
  Planarity :  0.005   0.051   1753
  Dihedral  :  4.898  32.986   1393
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.13 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.24), residues: 1244
  helix:  1.28 (0.25), residues: 408
  sheet:  0.37 (0.30), residues: 316
  loop : -0.07 (0.28), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E  36 
 HIS   0.009   0.002   HIS A 220 
 PHE   0.021   0.002   PHE R 286 
 TYR   0.018   0.002   TYR N  95 
 ARG   0.010   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  480)
  hydrogen bonds       : angle       4.64089 ( 1323)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.71831 (    4)
  covalent geometry    : bond        0.00507 (10198)
  covalent geometry    : angle       0.59686 (13818)
  Misc. bond           : bond        0.00236 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 263
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.7883 (ptp-110) cc_final: 0.7634 (ptp-110)
REVERT: A  266 LEU cc_start: 0.8355 (tp) cc_final: 0.7999 (tp)
REVERT: A  270 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8094 (mp)
REVERT: A  293 LYS cc_start: 0.8464 (mtpt) cc_final: 0.7793 (mtmt)
REVERT: A  343 LYS cc_start: 0.7648 (tttp) cc_final: 0.7005 (tttp)
REVERT: A  347 ASP cc_start: 0.7142 (m-30) cc_final: 0.6900 (m-30)
REVERT: A  370 GLU cc_start: 0.7711 (pm20) cc_final: 0.7401 (pm20)
REVERT: A  374 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7907 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8058 (t0) cc_final: 0.7593 (t0)
REVERT: A  391 TYR cc_start: 0.7972 (m-10) cc_final: 0.7725 (m-10)
REVERT: B   75 GLN cc_start: 0.8250 (mt0) cc_final: 0.7835 (mt0)
REVERT: B  135 VAL cc_start: 0.7980 (t) cc_final: 0.7750 (p)
REVERT: B  170 ASP cc_start: 0.7904 (t70) cc_final: 0.7632 (t70)
REVERT: B  239 ASN cc_start: 0.7984 (t0) cc_final: 0.7525 (t0)
REVERT: B  325 MET cc_start: 0.7820 (mmm) cc_final: 0.7399 (mmm)
REVERT: E  190 TYR cc_start: 0.8054 (p90) cc_final: 0.7731 (p90)
REVERT: N   28 THR cc_start: 0.8516 (m) cc_final: 0.7963 (p)
REVERT: N   94 TYR cc_start: 0.8281 (m-80) cc_final: 0.7926 (m-80)
  outliers start: 39
  outliers final: 28
  residues processed: 283
  average time/residue: 0.2365
  time to fit residues: 91.5972
Evaluate side-chains
  288 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 259
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  310 VAL
Chi-restraints excluded: chain R residue  318 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.147403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.129609 restraints weight = 14165.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 2.09
r_work: 0.3558 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3401 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10201  Z= 0.171
  Angle     :  0.579   7.001  13822  Z= 0.302
  Chirality :  0.044   0.245   1553
  Planarity :  0.005   0.075   1753
  Dihedral  :  4.818  31.757   1393
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.96 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.24), residues: 1244
  helix:  1.43 (0.25), residues: 403
  sheet:  0.29 (0.29), residues: 323
  loop : -0.07 (0.28), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.008   0.002   HIS A 220 
 PHE   0.019   0.002   PHE R 286 
 TYR   0.014   0.002   TYR R 313 
 ARG   0.010   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  480)
  hydrogen bonds       : angle       4.56117 ( 1323)
  SS BOND              : bond        0.00137 (    2)
  SS BOND              : angle       0.97121 (    4)
  covalent geometry    : bond        0.00388 (10198)
  covalent geometry    : angle       0.57872 (13818)
  Misc. bond           : bond        0.00198 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 260
  time to evaluate  : 1.353 
Fit side-chains
REVERT: A  266 LEU cc_start: 0.8337 (tp) cc_final: 0.7957 (tp)
REVERT: A  270 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  293 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7663 (mtmt)
REVERT: A  343 LYS cc_start: 0.7605 (tttp) cc_final: 0.6912 (tttp)
REVERT: A  347 ASP cc_start: 0.7164 (m-30) cc_final: 0.6905 (m-30)
REVERT: A  370 GLU cc_start: 0.7715 (pm20) cc_final: 0.7269 (pm20)
REVERT: A  374 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7918 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8002 (t0) cc_final: 0.7516 (t0)
REVERT: A  391 TYR cc_start: 0.7812 (m-10) cc_final: 0.7534 (m-10)
REVERT: B   68 ARG cc_start: 0.7425 (ptm-80) cc_final: 0.7074 (ttt-90)
REVERT: B   75 GLN cc_start: 0.8266 (mt0) cc_final: 0.7868 (mt0)
REVERT: B  170 ASP cc_start: 0.7846 (t70) cc_final: 0.7557 (t70)
REVERT: B  239 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7525 (t0)
REVERT: B  325 MET cc_start: 0.7679 (mmm) cc_final: 0.7232 (mmm)
REVERT: B  340 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7549 (t0)
REVERT: E  190 TYR cc_start: 0.8025 (p90) cc_final: 0.7705 (p90)
REVERT: N   28 THR cc_start: 0.8503 (m) cc_final: 0.7798 (p)
REVERT: N   32 TYR cc_start: 0.8456 (m-80) cc_final: 0.7799 (m-80)
REVERT: R  264 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8109 (mmm)
  outliers start: 40
  outliers final: 25
  residues processed: 283
  average time/residue: 0.2463
  time to fit residues: 97.0430
Evaluate side-chains
  282 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 253
  time to evaluate  : 1.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  226 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  127 THR
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  264 MET
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  310 VAL
Chi-restraints excluded: chain R residue  318 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0370
   chunk 51 optimal weight:    0.2980
   chunk 107 optimal weight:    0.6980
   chunk 115 optimal weight:    8.9990
   chunk 64 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B  88 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.149778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132001 restraints weight = 14089.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.09
r_work: 0.3596 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10201  Z= 0.126
  Angle     :  0.574   9.632  13822  Z= 0.298
  Chirality :  0.044   0.266   1553
  Planarity :  0.005   0.049   1753
  Dihedral  :  4.699  33.779   1393
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 19.89 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.24), residues: 1244
  helix:  1.53 (0.25), residues: 404
  sheet:  0.30 (0.29), residues: 324
  loop : -0.05 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.020   0.002   PHE R 286 
 TYR   0.014   0.001   TYR R 313 
 ARG   0.010   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  480)
  hydrogen bonds       : angle       4.44188 ( 1323)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.95118 (    4)
  covalent geometry    : bond        0.00281 (10198)
  covalent geometry    : angle       0.57338 (13818)
  Misc. bond           : bond        0.00221 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 248
  time to evaluate  : 2.202 
Fit side-chains
REVERT: A   39 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.7597 (ttm110)
REVERT: A   60 MET cc_start: 0.7070 (mmm) cc_final: 0.5995 (mmm)
REVERT: A  222 PHE cc_start: 0.7857 (m-80) cc_final: 0.7489 (m-80)
REVERT: A  266 LEU cc_start: 0.8315 (tp) cc_final: 0.7915 (tp)
REVERT: A  270 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  293 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7603 (mtmt)
REVERT: A  347 ASP cc_start: 0.7173 (m-30) cc_final: 0.6905 (m-30)
REVERT: A  370 GLU cc_start: 0.7693 (pm20) cc_final: 0.7263 (pm20)
REVERT: A  374 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7857 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8014 (t0) cc_final: 0.7500 (t0)
REVERT: B   68 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6921 (ttt180)
REVERT: B   75 GLN cc_start: 0.8173 (mt0) cc_final: 0.7817 (mt0)
REVERT: B  135 VAL cc_start: 0.7717 (t) cc_final: 0.7397 (p)
REVERT: B  170 ASP cc_start: 0.7804 (t70) cc_final: 0.7545 (t70)
REVERT: B  239 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7399 (t0)
REVERT: B  297 TRP cc_start: 0.8690 (m100) cc_final: 0.8436 (m100)
REVERT: E   27 PHE cc_start: 0.8073 (p90) cc_final: 0.7833 (p90)
REVERT: E  190 TYR cc_start: 0.8038 (p90) cc_final: 0.7670 (p90)
REVERT: N   28 THR cc_start: 0.8531 (m) cc_final: 0.7971 (p)
REVERT: N   34 MET cc_start: 0.7930 (mmm) cc_final: 0.7429 (mmm)
REVERT: N   83 MET cc_start: 0.7643 (mtt) cc_final: 0.7291 (mmm)
REVERT: R  213 MET cc_start: 0.5000 (pmm) cc_final: 0.2804 (ptt)
  outliers start: 30
  outliers final: 18
  residues processed: 263
  average time/residue: 0.3476
  time to fit residues: 126.1739
Evaluate side-chains
  268 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 248
  time to evaluate  : 2.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   93 VAL
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  301 SER
Chi-restraints excluded: chain R residue  310 VAL
Chi-restraints excluded: chain R residue  318 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    0.0270
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 84 optimal weight:    0.3980
   chunk 72 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0010
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.3844

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B  88 ASN
N  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.151114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133534 restraints weight = 14111.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 2.09
r_work: 0.3603 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10201  Z= 0.117
  Angle     :  0.572   8.832  13822  Z= 0.296
  Chirality :  0.043   0.264   1553
  Planarity :  0.005   0.049   1753
  Dihedral  :  4.572  31.223   1393
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.81 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.24), residues: 1244
  helix:  1.63 (0.26), residues: 401
  sheet:  0.45 (0.29), residues: 320
  loop : -0.08 (0.28), residues: 523

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 109 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.020   0.001   PHE R 286 
 TYR   0.014   0.001   TYR R 313 
 ARG   0.010   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  480)
  hydrogen bonds       : angle       4.37125 ( 1323)
  SS BOND              : bond        0.00181 (    2)
  SS BOND              : angle       0.98303 (    4)
  covalent geometry    : bond        0.00258 (10198)
  covalent geometry    : angle       0.57140 (13818)
  Misc. bond           : bond        0.00187 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.7830 (ptp-110) cc_final: 0.7563 (ttm110)
REVERT: A   60 MET cc_start: 0.6826 (mmm) cc_final: 0.6603 (mtt)
REVERT: A  221 MET cc_start: 0.7816 (mtm) cc_final: 0.7567 (mtm)
REVERT: A  222 PHE cc_start: 0.7886 (m-80) cc_final: 0.7579 (m-80)
REVERT: A  266 LEU cc_start: 0.8273 (tp) cc_final: 0.7882 (tp)
REVERT: A  270 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8023 (mp)
REVERT: A  336 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7120 (ttp80)
REVERT: A  343 LYS cc_start: 0.7516 (tttp) cc_final: 0.6910 (tttm)
REVERT: A  347 ASP cc_start: 0.7102 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  370 GLU cc_start: 0.7651 (pm20) cc_final: 0.7203 (pm20)
REVERT: A  374 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7752 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8015 (t0) cc_final: 0.7479 (t0)
REVERT: B   68 ARG cc_start: 0.7162 (ptm-80) cc_final: 0.6880 (ttt180)
REVERT: B   75 GLN cc_start: 0.8253 (mt0) cc_final: 0.7882 (mt0)
REVERT: B  170 ASP cc_start: 0.7830 (t70) cc_final: 0.7528 (t70)
REVERT: B  219 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7247 (ttm110)
REVERT: B  239 ASN cc_start: 0.7920 (t0) cc_final: 0.7295 (t0)
REVERT: B  297 TRP cc_start: 0.8674 (m100) cc_final: 0.8448 (m100)
REVERT: B  325 MET cc_start: 0.7604 (mmm) cc_final: 0.7234 (mmm)
REVERT: E   27 PHE cc_start: 0.8100 (p90) cc_final: 0.7888 (p90)
REVERT: E  190 TYR cc_start: 0.7974 (p90) cc_final: 0.7543 (p90)
REVERT: N   28 THR cc_start: 0.8545 (m) cc_final: 0.8017 (p)
REVERT: N   34 MET cc_start: 0.7945 (mmm) cc_final: 0.7414 (mmm)
REVERT: N   83 MET cc_start: 0.7637 (mtt) cc_final: 0.7225 (mmm)
REVERT: R  213 MET cc_start: 0.4879 (pmm) cc_final: 0.2719 (ptt)
  outliers start: 23
  outliers final: 18
  residues processed: 258
  average time/residue: 0.2669
  time to fit residues: 94.1888
Evaluate side-chains
  261 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 242
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  127 THR
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  310 VAL
Chi-restraints excluded: chain R residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 121 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 362 HIS
B  88 ASN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.151487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.134057 restraints weight = 13981.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.12
r_work: 0.3621 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10201  Z= 0.147
  Angle     :  0.586   9.581  13822  Z= 0.304
  Chirality :  0.044   0.256   1553
  Planarity :  0.005   0.048   1753
  Dihedral  :  4.627  31.256   1393
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.18 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.24), residues: 1244
  helix:  1.59 (0.25), residues: 401
  sheet:  0.54 (0.30), residues: 314
  loop : -0.15 (0.28), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.008   0.001   HIS A 220 
 PHE   0.020   0.002   PHE R 286 
 TYR   0.025   0.002   TYR B 145 
 ARG   0.012   0.001   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  480)
  hydrogen bonds       : angle       4.39769 ( 1323)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       1.05866 (    4)
  covalent geometry    : bond        0.00333 (10198)
  covalent geometry    : angle       0.58560 (13818)
  Misc. bond           : bond        0.00200 (    1)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 250
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ARG cc_start: 0.7856 (ptp-110) cc_final: 0.7612 (ttm110)
REVERT: A   60 MET cc_start: 0.6870 (mmm) cc_final: 0.6628 (mtt)
REVERT: A  221 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7626 (mtm)
REVERT: A  222 PHE cc_start: 0.7995 (m-80) cc_final: 0.7637 (m-80)
REVERT: A  266 LEU cc_start: 0.8212 (tp) cc_final: 0.7908 (tp)
REVERT: A  270 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7956 (mp)
REVERT: A  333 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7146 (mtm-85)
REVERT: A  336 ARG cc_start: 0.7471 (ttt-90) cc_final: 0.7075 (ttp80)
REVERT: A  343 LYS cc_start: 0.7645 (tttp) cc_final: 0.6997 (tttm)
REVERT: A  347 ASP cc_start: 0.7129 (m-30) cc_final: 0.6893 (m-30)
REVERT: A  370 GLU cc_start: 0.7652 (pm20) cc_final: 0.7164 (pm20)
REVERT: A  374 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7823 (mtm-85)
REVERT: A  381 ASP cc_start: 0.8031 (t0) cc_final: 0.7494 (t0)
REVERT: A  391 TYR cc_start: 0.7682 (m-10) cc_final: 0.7398 (m-10)
REVERT: B   75 GLN cc_start: 0.8436 (mt0) cc_final: 0.8100 (mt0)
REVERT: B  135 VAL cc_start: 0.7713 (t) cc_final: 0.7407 (p)
REVERT: B  170 ASP cc_start: 0.7881 (t70) cc_final: 0.7506 (t70)
REVERT: B  219 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7306 (ttm110)
REVERT: B  239 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7125 (t0)
REVERT: B  325 MET cc_start: 0.7727 (mmm) cc_final: 0.7325 (mmm)
REVERT: E   27 PHE cc_start: 0.8139 (p90) cc_final: 0.7910 (p90)
REVERT: E  190 TYR cc_start: 0.7912 (p90) cc_final: 0.7422 (p90)
REVERT: G   47 GLU cc_start: 0.7543 (mp0) cc_final: 0.7281 (mp0)
REVERT: N   28 THR cc_start: 0.8505 (m) cc_final: 0.7927 (p)
REVERT: N   34 MET cc_start: 0.7987 (mmm) cc_final: 0.7451 (mmm)
REVERT: R  213 MET cc_start: 0.5025 (pmm) cc_final: 0.2991 (ptt)
REVERT: R  264 MET cc_start: 0.8354 (tpp) cc_final: 0.8053 (tpp)
  outliers start: 22
  outliers final: 19
  residues processed: 263
  average time/residue: 0.2447
  time to fit residues: 87.2805
Evaluate side-chains
  272 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 250
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 ASN
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   71 SER
Chi-restraints excluded: chain N residue  126 VAL
Chi-restraints excluded: chain R residue   42 LEU
Chi-restraints excluded: chain R residue  119 PHE
Chi-restraints excluded: chain R residue  120 GLN
Chi-restraints excluded: chain R residue  127 THR
Chi-restraints excluded: chain R residue  130 THR
Chi-restraints excluded: chain R residue  198 CYS
Chi-restraints excluded: chain R residue  310 VAL
Chi-restraints excluded: chain R residue  318 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0060
   chunk 30 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0770
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.4154

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 362 HIS
B  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.152700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.135464 restraints weight = 13930.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.11
r_work: 0.3652 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3499 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10201  Z= 0.115
  Angle     :  0.572   9.152  13822  Z= 0.294
  Chirality :  0.043   0.260   1553
  Planarity :  0.005   0.049   1753
  Dihedral  :  4.509  30.244   1393
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.81 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.44 %
    Cis-general     : 0.25 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.24), residues: 1244
  helix:  1.65 (0.26), residues: 401
  sheet:  0.52 (0.29), residues: 329
  loop : -0.15 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.023   0.001   PHE R 286 
 TYR   0.019   0.001   TYR B 145 
 ARG   0.010   0.001   ARG A 333 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  480)
  hydrogen bonds       : angle       4.31601 ( 1323)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       0.99357 (    4)
  covalent geometry    : bond        0.00253 (10198)
  covalent geometry    : angle       0.57185 (13818)
  Misc. bond           : bond        0.00183 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6987.60 seconds
wall clock time: 129 minutes 13.15 seconds (7753.15 seconds total)