Starting phenix.real_space_refine
on Mon Jul 28 22:28:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ra3_24334/07_2025/7ra3_24334_neut.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    6859      2.51       5
     N    1894      2.21       5
     O    1985      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10802
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1792
          Classifications: {'peptide': 220}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 6, 'TRANS': 213}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "B"
      Number of atoms: 2581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2581
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 24
    Chain: "E"
      Number of atoms: 1747
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1747
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "G"
      Number of atoms: 453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 453
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
    Chain: "N"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
    Chain: "P"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 262
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "R"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 3001
          Classifications: {'peptide': 371}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 14, 'TRANS': 356}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA R  53 " occ=0.70
      ... (3 atoms not shown)
      pdb=" CB  ALA R  53 " occ=0.70
  Time building chain proxies: 7.30, per 1000 atoms: 0.68
  Number of scatterers: 10802
  At special positions: 0
  Unit cell: (167.184, 123.12, 104.976, 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    1985      8.00
     N    1894      7.00
     C    6859      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  46 " - pdb=" SG  CYS R  70 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R  61 " - pdb=" SG  CYS R 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  84 " - pdb=" SG  CYS R 118 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 216 " - pdb=" SG  CYS R 286 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2570

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 16 sheets defined
      36.6% alpha, 20.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 38
      removed outlier: 3.541A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
      removed outlier: 3.778A  pdb=" N   LYS A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 54 through 59'
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.677A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ASP A 240 " --> pdb=" O   CYS A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.820A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 4.158A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.832A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 391
      removed outlier: 3.861A  pdb=" N   VAL A 375 " --> pdb=" O   ASN A 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 35
      removed outlier: 3.797A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.840A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 62 through 65
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.591A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.817A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.619A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 2 through 29
    Processing helix  chain 'P' and resid 30 through 32
      No H-bonds generated for 'chain 'P' and resid 30 through 32'
    Processing helix  chain 'R' and resid 31 through 53
      removed outlier: 3.782A  pdb=" N   GLN R  37 " --> pdb=" O   GLY R  33 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR R  42 " --> pdb=" O   ARG R  38 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLU R  48 " --> pdb=" O   ARG R  44 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR R  49 " --> pdb=" O   GLU R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 88 through 93
      removed outlier: 4.083A  pdb=" N   HIS R  92 " --> pdb=" O   PRO R  89 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 162
      removed outlier: 4.321A  pdb=" N   PHE R 162 " --> pdb=" O   ILE R 158 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 167 through 194
    Processing helix  chain 'R' and resid 208 through 246
    Processing helix  chain 'R' and resid 253 through 281
      removed outlier: 3.634A  pdb=" N   LEU R 261 " --> pdb=" O   ARG R 257 " (cutoff:3.500A)
      Proline residue:  R 267  - end of helix
      removed outlier: 3.787A  pdb=" N   ILE R 272 " --> pdb=" O   ALA R 268 " (cutoff:3.500A)
      Proline residue:  R 273  - end of helix
    Processing helix  chain 'R' and resid 292 through 328
      removed outlier: 3.609A  pdb=" N   TRP R 296 " --> pdb=" O   VAL R 292 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE R 298 " --> pdb=" O   ALA R 294 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 336 through 351
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 352 through 356
    Processing helix  chain 'R' and resid 362 through 367
    Processing helix  chain 'R' and resid 370 through 393
      removed outlier: 3.758A  pdb=" N   PHE R 376 " --> pdb=" O   ALA R 372 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   GLU R 377 " --> pdb=" O   LYS R 373 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   GLY R 385 " --> pdb=" O   SER R 381 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   PHE R 386 " --> pdb=" O   SER R 382 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 396 through 410
      removed outlier: 3.743A  pdb=" N   HIS R 408 " --> pdb=" O   ARG R 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213
      removed outlier: 3.589A  pdb=" N   PHE A 222 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR A 360 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.871A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ALA B 328 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   LEU B 318 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.929A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.855A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 149
      removed outlier: 4.430A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.178A  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: 4.102A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.720A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 6.566A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.739A  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
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.094A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 129
      removed outlier: 3.565A  pdb=" N   ARG E 148 " --> pdb=" O   THR E 129 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 135
      removed outlier: 3.672A  pdb=" N   VAL E 135 " --> pdb=" O   LYS E 232 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'E' and resid 182 through 183
      removed outlier: 6.654A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB6, first strand: chain 'N' and resid 59 through 60
      removed outlier: 6.604A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'R' and resid 78 through 80

    518 hydrogen bonds defined for protein.
    1431 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: 3.62

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2019
        1.33 -     1.45: 2954
        1.45 -     1.57: 5977
        1.57 -     1.70: 1
        1.70 -     1.82: 89
  Bond restraints: 11040
  Sorted by residual:
  bond pdb=" C   THR B 243 "
       pdb=" N   GLY B 244 "
    ideal  model  delta    sigma   weight residual
    1.331  1.312  0.019 6.60e-03 2.30e+04 8.56e+00
  bond pdb=" N   ASP B 247 "
       pdb=" CA  ASP B 247 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.32e-02 5.74e+03 7.12e+00
  bond pdb=" C   PRO G  49 "
       pdb=" O   PRO G  49 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.30e-02 5.92e+03 5.92e+00
  bond pdb=" C   THR B 243 "
       pdb=" O   THR B 243 "
    ideal  model  delta    sigma   weight residual
    1.235  1.207  0.027 1.13e-02 7.83e+03 5.86e+00
  bond pdb=" N   ASP G  48 "
       pdb=" CA  ASP G  48 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.25e-02 6.40e+03 4.35e+00
  ... (remaining 11035 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 14498
        2.29 -     4.59: 384
        4.59 -     6.88: 85
        6.88 -     9.17: 6
        9.17 -    11.47: 2
  Bond angle restraints: 14975
  Sorted by residual:
  angle pdb=" C   ASP G  48 "
        pdb=" CA  ASP G  48 "
        pdb=" CB  ASP G  48 "
      ideal   model   delta    sigma   weight residual
     110.17  103.94    6.23 1.11e+00 8.12e-01 3.15e+01
  angle pdb=" N   GLN R 285 "
        pdb=" CA  GLN R 285 "
        pdb=" C   GLN R 285 "
      ideal   model   delta    sigma   weight residual
     110.80   99.33   11.47 2.13e+00 2.20e-01 2.90e+01
  angle pdb=" CA  ARG G  13 "
        pdb=" CB  ARG G  13 "
        pdb=" CG  ARG G  13 "
      ideal   model   delta    sigma   weight residual
     114.10  122.96   -8.86 2.00e+00 2.50e-01 1.96e+01
  angle pdb=" CB  GLN R 285 "
        pdb=" CG  GLN R 285 "
        pdb=" CD  GLN R 285 "
      ideal   model   delta    sigma   weight residual
     112.60  119.85   -7.25 1.70e+00 3.46e-01 1.82e+01
  angle pdb=" CA  GLU A 230 "
        pdb=" C   GLU A 230 "
        pdb=" O   GLU A 230 "
      ideal   model   delta    sigma   weight residual
     121.58  116.92    4.66 1.12e+00 7.97e-01 1.73e+01
  ... (remaining 14970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 5804
       16.54 -    33.08: 583
       33.08 -    49.62: 104
       49.62 -    66.16: 13
       66.16 -    82.70: 11
  Dihedral angle restraints: 6515
    sinusoidal: 2523
      harmonic: 3992
  Sorted by residual:
  dihedral pdb=" CB  CYS R 216 "
           pdb=" SG  CYS R 216 "
           pdb=" SG  CYS R 286 "
           pdb=" CB  CYS R 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.26  -50.26     1      1.00e+01 1.00e-02 3.46e+01
  dihedral pdb=" CA  ARG N  38 "
           pdb=" C   ARG N  38 "
           pdb=" N   GLN N  39 "
           pdb=" CA  GLN N  39 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.19   24.81     0      5.00e+00 4.00e-02 2.46e+01
  dihedral pdb=" CA  LYS A 211 "
           pdb=" C   LYS A 211 "
           pdb=" N   PHE A 212 "
           pdb=" CA  PHE A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.22   24.78     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 6512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1194
       0.045 -    0.091: 348
       0.091 -    0.136: 107
       0.136 -    0.181: 15
       0.181 -    0.226: 3
  Chirality restraints: 1667
  Sorted by residual:
  chirality pdb=" CG  LEU A 388 "
            pdb=" CB  LEU A 388 "
            pdb=" CD1 LEU A 388 "
            pdb=" CD2 LEU A 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CG  LEU B 261 "
            pdb=" CB  LEU B 261 "
            pdb=" CD1 LEU B 261 "
            pdb=" CD2 LEU B 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.97e-01
  ... (remaining 1664 not shown)

  Planarity restraints: 1909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 111 "    0.013 2.00e-02 2.50e+03   2.23e-02 1.24e+01
        pdb=" CG  TRP E 111 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 111 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 111 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 111 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 111 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 111 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 111 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.025 2.00e-02 2.50e+03   2.23e-02 9.96e+00
        pdb=" CG  TYR B  59 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R  75 "   -0.050 5.00e-02 4.00e+02   7.54e-02 9.09e+00
        pdb=" N   PRO R  76 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO R  76 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO R  76 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1906 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 181
        2.64 -     3.20: 10500
        3.20 -     3.77: 17195
        3.77 -     4.33: 23312
        4.33 -     4.90: 38344
  Nonbonded interactions: 89532
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.074 3.040
  nonbonded pdb=" ND2 ASN R 310 "
            pdb=" O   LEU R 350 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   PRO A 332 "
            pdb=" OG1 THR A 335 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   GLN E 113 "
            pdb=" OG  SER E 172 "
     model   vdw
     2.260 3.040
  ... (remaining 89527 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=0.50 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:             39.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.400
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
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      :  0.005   0.086  11048  Z= 0.258
  Angle     :  0.907  11.467  14991  Z= 0.481
  Chirality :  0.048   0.226   1667
  Planarity :  0.005   0.075   1909
  Dihedral  : 13.678  82.697   3921
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.35 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.23), residues: 1349
  helix: -0.50 (0.23), residues: 446
  sheet: -1.67 (0.26), residues: 350
  loop : -1.39 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP E 111 
 HIS   0.019   0.002   HIS A 357 
 PHE   0.033   0.002   PHE P   6 
 TYR   0.055   0.002   TYR B  59 
 ARG   0.033   0.001   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13399 (  518)
  hydrogen bonds       : angle       6.87814 ( 1431)
  SS BOND              : bond        0.00491 (    8)
  SS BOND              : angle       1.80926 (   16)
  covalent geometry    : bond        0.00540 (11040)
  covalent geometry    : angle       0.90533 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 213
  time to evaluate  : 1.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   24 ASN cc_start: 0.8967 (m110) cc_final: 0.8643 (m-40)
REVERT: R  237 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8084 (tm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 215
  average time/residue: 0.2917
  time to fit residues: 85.8640
Evaluate side-chains
  163 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 1.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 102 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 78 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
E 130 GLN
E 171 GLN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  29 GLN
R 230 ASN
R 384 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.093226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.072711 restraints weight = 33787.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 3.02
r_work: 0.3267 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  11048  Z= 0.215
  Angle     :  0.735  11.444  14991  Z= 0.378
  Chirality :  0.046   0.185   1667
  Planarity :  0.005   0.058   1909
  Dihedral  :  5.504  39.529   1515
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.31 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.65 (0.23), residues: 1349
  helix: -0.24 (0.24), residues: 440
  sheet: -1.46 (0.27), residues: 340
  loop : -1.40 (0.28), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP E 111 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.016   0.002   PHE N  68 
 TYR   0.026   0.002   TYR R 259 
 ARG   0.009   0.001   ARG A 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  518)
  hydrogen bonds       : angle       5.53692 ( 1431)
  SS BOND              : bond        0.00577 (    8)
  SS BOND              : angle       2.98744 (   16)
  covalent geometry    : bond        0.00483 (11040)
  covalent geometry    : angle       0.72858 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  151 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8205 (ptpt)
REVERT: G   36 ASP cc_start: 0.8172 (m-30) cc_final: 0.7846 (t70)
REVERT: N   18 LEU cc_start: 0.7661 (mt) cc_final: 0.7292 (mt)
REVERT: N   69 THR cc_start: 0.8552 (m) cc_final: 0.8200 (t)
REVERT: P   24 ASN cc_start: 0.8967 (m110) cc_final: 0.8593 (m-40)
REVERT: R  237 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8293 (tm-30)
  outliers start: 24
  outliers final: 15
  residues processed: 190
  average time/residue: 0.2583
  time to fit residues: 69.9311
Evaluate side-chains
  171 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    9.9990
   chunk 133 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 72 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0170
   chunk 117 optimal weight:    3.9990
   chunk 129 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
E 171 GLN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  44 HIS
R 242 HIS
R 384 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.093433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.073145 restraints weight = 34338.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.04
r_work: 0.3274 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3277
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3277 r_free = 0.3277    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3277
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11048  Z= 0.176
  Angle     :  0.688  11.111  14991  Z= 0.351
  Chirality :  0.044   0.180   1667
  Planarity :  0.004   0.055   1909
  Dihedral  :  5.099  37.221   1514
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.27 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.39 (0.23), residues: 1349
  helix:  0.08 (0.24), residues: 437
  sheet: -1.33 (0.27), residues: 342
  loop : -1.31 (0.28), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 111 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.026   0.002   PHE P   6 
 TYR   0.022   0.002   TYR R 259 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  518)
  hydrogen bonds       : angle       5.22403 ( 1431)
  SS BOND              : bond        0.00342 (    8)
  SS BOND              : angle       3.17816 (   16)
  covalent geometry    : bond        0.00392 (11040)
  covalent geometry    : angle       0.68057 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 176
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  198 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8659 (pp)
REVERT: B  210 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8462 (tp)
REVERT: E  171 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7377 (pm20)
REVERT: G   14 LYS cc_start: 0.9070 (mtmm) cc_final: 0.8827 (mtmm)
REVERT: G   36 ASP cc_start: 0.8181 (m-30) cc_final: 0.7924 (t70)
REVERT: N   11 LEU cc_start: 0.8662 (mt) cc_final: 0.8399 (mp)
REVERT: N   69 THR cc_start: 0.8550 (m) cc_final: 0.8223 (p)
REVERT: P   24 ASN cc_start: 0.9012 (m110) cc_final: 0.8581 (m-40)
REVERT: R  165 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6662 (pp)
REVERT: R  237 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8316 (tm-30)
  outliers start: 39
  outliers final: 20
  residues processed: 203
  average time/residue: 0.2165
  time to fit residues: 64.8726
Evaluate side-chains
  184 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  171 GLN
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 101 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
E 171 GLN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.094773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.074549 restraints weight = 33799.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 3.05
r_work: 0.3306 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11048  Z= 0.134
  Angle     :  0.666   9.070  14991  Z= 0.336
  Chirality :  0.043   0.186   1667
  Planarity :  0.004   0.053   1909
  Dihedral  :  4.831  38.021   1514
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.68 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.25 (0.23), residues: 1349
  helix:  0.27 (0.25), residues: 440
  sheet: -1.21 (0.27), residues: 333
  loop : -1.36 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 111 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.016   0.001   PHE A 212 
 TYR   0.020   0.001   TYR R 259 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03640 (  518)
  hydrogen bonds       : angle       4.99212 ( 1431)
  SS BOND              : bond        0.00307 (    8)
  SS BOND              : angle       2.87559 (   16)
  covalent geometry    : bond        0.00296 (11040)
  covalent geometry    : angle       0.65927 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.8001 (p0) cc_final: 0.6827 (t70)
REVERT: B  198 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8561 (pp)
REVERT: B  210 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8411 (tp)
REVERT: G   20 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (ptpp)
REVERT: G   36 ASP cc_start: 0.8105 (m-30) cc_final: 0.7899 (t70)
REVERT: N   11 LEU cc_start: 0.8635 (mt) cc_final: 0.8398 (mp)
REVERT: N   69 THR cc_start: 0.8526 (m) cc_final: 0.8278 (p)
REVERT: N  123 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8700 (tm-30)
REVERT: P   24 ASN cc_start: 0.9030 (m110) cc_final: 0.8614 (m110)
REVERT: R  165 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6625 (pp)
  outliers start: 42
  outliers final: 26
  residues processed: 217
  average time/residue: 0.2723
  time to fit residues: 86.8022
Evaluate side-chains
  202 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 102 optimal weight:   20.0000
   chunk 126 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.093720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.073426 restraints weight = 33810.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.03
r_work: 0.3280 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11048  Z= 0.174
  Angle     :  0.687   9.135  14991  Z= 0.348
  Chirality :  0.044   0.211   1667
  Planarity :  0.004   0.053   1909
  Dihedral  :  4.800  35.971   1514
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 18.91 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.12 (0.23), residues: 1349
  helix:  0.42 (0.25), residues: 436
  sheet: -1.15 (0.28), residues: 331
  loop : -1.30 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 111 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.022   0.002   PHE P   6 
 TYR   0.022   0.002   TYR R 259 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  518)
  hydrogen bonds       : angle       4.94639 ( 1431)
  SS BOND              : bond        0.00324 (    8)
  SS BOND              : angle       2.91254 (   16)
  covalent geometry    : bond        0.00393 (11040)
  covalent geometry    : angle       0.68033 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 188
  time to evaluate  : 1.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.8026 (p0) cc_final: 0.6820 (t70)
REVERT: B  198 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8578 (pp)
REVERT: B  210 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8444 (tp)
REVERT: G   36 ASP cc_start: 0.8145 (m-30) cc_final: 0.7925 (t70)
REVERT: N   69 THR cc_start: 0.8618 (m) cc_final: 0.8372 (p)
REVERT: N  123 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8761 (tm-30)
REVERT: P    1 TYR cc_start: 0.8106 (p90) cc_final: 0.7806 (p90)
REVERT: P   24 ASN cc_start: 0.9050 (m110) cc_final: 0.8684 (m110)
REVERT: R  159 LEU cc_start: 0.8330 (tp) cc_final: 0.7748 (mp)
REVERT: R  165 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6836 (pp)
  outliers start: 51
  outliers final: 33
  residues processed: 225
  average time/residue: 0.2135
  time to fit residues: 69.3632
Evaluate side-chains
  208 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 74 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   1 GLN
R 384 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.092801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.072726 restraints weight = 33622.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 3.00
r_work: 0.3258 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  11048  Z= 0.201
  Angle     :  0.702   8.707  14991  Z= 0.356
  Chirality :  0.045   0.226   1667
  Planarity :  0.004   0.054   1909
  Dihedral  :  4.849  33.374   1514
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 19.44 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.11 (0.23), residues: 1349
  helix:  0.44 (0.25), residues: 432
  sheet: -1.13 (0.28), residues: 332
  loop : -1.31 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.018   0.002   PHE P   6 
 TYR   0.021   0.002   TYR R 259 
 ARG   0.005   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  518)
  hydrogen bonds       : angle       4.94557 ( 1431)
  SS BOND              : bond        0.00335 (    8)
  SS BOND              : angle       2.70926 (   16)
  covalent geometry    : bond        0.00452 (11040)
  covalent geometry    : angle       0.69683 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 182
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8929 (mtpp)
REVERT: A  295 ASP cc_start: 0.7926 (p0) cc_final: 0.6888 (t70)
REVERT: B  210 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8446 (tp)
REVERT: G   36 ASP cc_start: 0.8273 (m-30) cc_final: 0.7972 (t70)
REVERT: N   69 THR cc_start: 0.8650 (m) cc_final: 0.8408 (p)
REVERT: N  123 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8761 (tm-30)
REVERT: P    1 TYR cc_start: 0.8169 (p90) cc_final: 0.7900 (p90)
REVERT: P   14 MET cc_start: 0.8355 (mmm) cc_final: 0.7998 (mmm)
REVERT: P   24 ASN cc_start: 0.9067 (m110) cc_final: 0.8702 (m110)
REVERT: R  159 LEU cc_start: 0.8367 (tp) cc_final: 0.7769 (mp)
REVERT: R  165 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6865 (pp)
  outliers start: 57
  outliers final: 38
  residues processed: 222
  average time/residue: 0.2035
  time to fit residues: 65.8225
Evaluate side-chains
  215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 111 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 115 optimal weight:   20.0000
   chunk 131 optimal weight:    0.9990
   chunk 107 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.093486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.073188 restraints weight = 34230.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.04
r_work: 0.3276 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11048  Z= 0.172
  Angle     :  0.696   8.010  14991  Z= 0.350
  Chirality :  0.044   0.248   1667
  Planarity :  0.004   0.050   1909
  Dihedral  :  4.806  35.444   1514
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 20.32 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -1.03 (0.23), residues: 1349
  helix:  0.49 (0.25), residues: 434
  sheet: -1.06 (0.28), residues: 332
  loop : -1.26 (0.28), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.017   0.001   PHE P   6 
 TYR   0.020   0.002   TYR R 259 
 ARG   0.004   0.000   ARG B   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  518)
  hydrogen bonds       : angle       4.87911 ( 1431)
  SS BOND              : bond        0.00319 (    8)
  SS BOND              : angle       2.77570 (   16)
  covalent geometry    : bond        0.00386 (11040)
  covalent geometry    : angle       0.69013 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 1.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9189 (mtpp) cc_final: 0.8939 (mtpp)
REVERT: A  295 ASP cc_start: 0.7892 (p0) cc_final: 0.6872 (t70)
REVERT: B  210 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8451 (tp)
REVERT: G   36 ASP cc_start: 0.8178 (m-30) cc_final: 0.7953 (t70)
REVERT: N   69 THR cc_start: 0.8625 (m) cc_final: 0.8361 (p)
REVERT: N  123 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8749 (tm-30)
REVERT: P    1 TYR cc_start: 0.8138 (p90) cc_final: 0.7922 (p90)
REVERT: P   14 MET cc_start: 0.8320 (mmm) cc_final: 0.7921 (mmm)
REVERT: P   15 ASP cc_start: 0.8950 (t70) cc_final: 0.8484 (t70)
REVERT: P   24 ASN cc_start: 0.9060 (m110) cc_final: 0.8692 (m110)
REVERT: R  165 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6637 (pp)
  outliers start: 49
  outliers final: 38
  residues processed: 214
  average time/residue: 0.2200
  time to fit residues: 67.8028
Evaluate side-chains
  220 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 180
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0010
   chunk 78 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 103 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9990
   overall best weight:    1.1992

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.094797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.074719 restraints weight = 33651.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.99
r_work: 0.3311 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11048  Z= 0.138
  Angle     :  0.681   8.240  14991  Z= 0.339
  Chirality :  0.043   0.262   1667
  Planarity :  0.004   0.049   1909
  Dihedral  :  4.659  35.038   1514
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 20.76 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.92 (0.24), residues: 1349
  helix:  0.62 (0.25), residues: 434
  sheet: -0.97 (0.30), residues: 307
  loop : -1.26 (0.27), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 111 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.018   0.001   PHE A 222 
 TYR   0.019   0.001   TYR R 259 
 ARG   0.005   0.000   ARG N  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  518)
  hydrogen bonds       : angle       4.78861 ( 1431)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       2.52886 (   16)
  covalent geometry    : bond        0.00307 (11040)
  covalent geometry    : angle       0.67661 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 194
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8926 (mtpp)
REVERT: A  295 ASP cc_start: 0.7875 (p0) cc_final: 0.6863 (t70)
REVERT: B  210 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8454 (tp)
REVERT: E   93 MET cc_start: 0.8219 (tpt) cc_final: 0.7914 (tpt)
REVERT: G   36 ASP cc_start: 0.8187 (m-30) cc_final: 0.7933 (t70)
REVERT: N   69 THR cc_start: 0.8620 (m) cc_final: 0.8368 (p)
REVERT: N   73 ASP cc_start: 0.7939 (t0) cc_final: 0.7482 (t70)
REVERT: N  123 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: P   14 MET cc_start: 0.8256 (mmm) cc_final: 0.8013 (mmm)
REVERT: P   15 ASP cc_start: 0.8906 (t70) cc_final: 0.8442 (t70)
REVERT: P   24 ASN cc_start: 0.9052 (m110) cc_final: 0.8698 (m110)
REVERT: R  164 ARG cc_start: 0.7138 (ttt-90) cc_final: 0.6907 (mpt180)
REVERT: R  165 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6766 (pp)
REVERT: R  405 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.5869 (ttp80)
  outliers start: 51
  outliers final: 35
  residues processed: 223
  average time/residue: 0.2196
  time to fit residues: 70.0508
Evaluate side-chains
  221 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 183
  time to evaluate  : 1.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Chi-restraints excluded: chain R residue  405 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 48 optimal weight:   10.0000
   chunk 76 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 219 GLN
E 220 HIS
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.093526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.073153 restraints weight = 34062.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.06
r_work: 0.3275 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11048  Z= 0.192
  Angle     :  0.720   9.488  14991  Z= 0.363
  Chirality :  0.045   0.268   1667
  Planarity :  0.004   0.050   1909
  Dihedral  :  4.788  32.261   1514
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 20.93 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.98 (0.23), residues: 1349
  helix:  0.56 (0.25), residues: 434
  sheet: -1.01 (0.29), residues: 307
  loop : -1.28 (0.27), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.029   0.002   PHE A 222 
 TYR   0.033   0.002   TYR R  87 
 ARG   0.004   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  518)
  hydrogen bonds       : angle       4.87606 ( 1431)
  SS BOND              : bond        0.00351 (    8)
  SS BOND              : angle       2.46638 (   16)
  covalent geometry    : bond        0.00434 (11040)
  covalent geometry    : angle       0.71590 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8938 (mtpp)
REVERT: A  295 ASP cc_start: 0.7916 (p0) cc_final: 0.6935 (t70)
REVERT: B  210 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8466 (tp)
REVERT: B  270 ILE cc_start: 0.8595 (tp) cc_final: 0.8307 (tp)
REVERT: E   93 MET cc_start: 0.8275 (tpt) cc_final: 0.8043 (tpt)
REVERT: G   36 ASP cc_start: 0.8292 (m-30) cc_final: 0.7974 (t70)
REVERT: N   69 THR cc_start: 0.8616 (m) cc_final: 0.8358 (p)
REVERT: N  123 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: P   15 ASP cc_start: 0.8978 (t70) cc_final: 0.8497 (t70)
REVERT: P   24 ASN cc_start: 0.9058 (m110) cc_final: 0.8707 (m110)
REVERT: R  164 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6935 (mpt180)
REVERT: R  165 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6686 (pp)
REVERT: R  405 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5945 (ttp-170)
  outliers start: 50
  outliers final: 40
  residues processed: 210
  average time/residue: 0.2788
  time to fit residues: 86.5688
Evaluate side-chains
  215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 172
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Chi-restraints excluded: chain R residue  405 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 120 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 77 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0020
   chunk 67 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 123 optimal weight:    4.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 219 GLN
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 384 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.095446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.075366 restraints weight = 33612.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.99
r_work: 0.3324 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11048  Z= 0.131
  Angle     :  0.704  11.782  14991  Z= 0.348
  Chirality :  0.044   0.275   1667
  Planarity :  0.004   0.048   1909
  Dihedral  :  4.632  31.065   1514
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 21.81 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    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: -0.85 (0.24), residues: 1349
  helix:  0.64 (0.25), residues: 442
  sheet: -0.84 (0.30), residues: 298
  loop : -1.26 (0.27), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.023   0.001   PHE A 222 
 TYR   0.027   0.002   TYR R  87 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  518)
  hydrogen bonds       : angle       4.75459 ( 1431)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       2.32724 (   16)
  covalent geometry    : bond        0.00292 (11040)
  covalent geometry    : angle       0.70020 (14975)

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

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

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2698 Ramachandran restraints generated.
    1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 186
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8910 (mtpp)
REVERT: A  295 ASP cc_start: 0.7883 (p0) cc_final: 0.6896 (t70)
REVERT: B  210 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8483 (tp)
REVERT: E   93 MET cc_start: 0.8235 (tpt) cc_final: 0.7976 (tpt)
REVERT: G   36 ASP cc_start: 0.8266 (m-30) cc_final: 0.7919 (t70)
REVERT: N   69 THR cc_start: 0.8508 (m) cc_final: 0.8296 (p)
REVERT: N  123 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8726 (tm-30)
REVERT: P   15 ASP cc_start: 0.8882 (t70) cc_final: 0.8396 (t70)
REVERT: P   24 ASN cc_start: 0.9075 (m110) cc_final: 0.8713 (m-40)
REVERT: R  164 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6944 (mpt180)
REVERT: R  165 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6638 (pp)
REVERT: R  405 ARG cc_start: 0.6746 (OUTLIER) cc_final: 0.5900 (ttp80)
  outliers start: 47
  outliers final: 38
  residues processed: 213
  average time/residue: 0.2651
  time to fit residues: 79.4463
Evaluate side-chains
  221 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  211 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain P residue    7 ILE
Chi-restraints excluded: chain P residue   11 SER
Chi-restraints excluded: chain R residue   72 ASP
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  147 LEU
Chi-restraints excluded: chain R residue  153 LEU
Chi-restraints excluded: chain R residue  165 LEU
Chi-restraints excluded: chain R residue  187 ILE
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  339 LEU
Chi-restraints excluded: chain R residue  360 VAL
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  393 CYS
Chi-restraints excluded: chain R residue  405 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 132 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 109 optimal weight:    8.9990
   chunk 128 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 98 optimal weight:    0.0060
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.096376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.076254 restraints weight = 33657.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 3.08
r_work: 0.3345 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11048  Z= 0.125
  Angle     :  0.710  11.387  14991  Z= 0.350
  Chirality :  0.043   0.288   1667
  Planarity :  0.004   0.048   1909
  Dihedral  :  4.541  28.615   1514
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.25 %
    Favored  : 74.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.24), residues: 1349
  helix:  0.65 (0.25), residues: 442
  sheet: -0.74 (0.31), residues: 292
  loop : -1.26 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 339 
 HIS   0.006   0.001   HIS B 266 
 PHE   0.027   0.001   PHE A 222 
 TYR   0.025   0.001   TYR R  87 
 ARG   0.006   0.000   ARG G  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  518)
  hydrogen bonds       : angle       4.71821 ( 1431)
  SS BOND              : bond        0.00294 (    8)
  SS BOND              : angle       2.13938 (   16)
  covalent geometry    : bond        0.00277 (11040)
  covalent geometry    : angle       0.70720 (14975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6750.58 seconds
wall clock time: 122 minutes 48.66 seconds (7368.66 seconds total)