Starting phenix.real_space_refine
on Wed Mar  4 04:12:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ra3_24334/03_2026/7ra3_24334_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ra3_24334/03_2026/7ra3_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_24334/03_2026/7ra3_24334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ra3_24334/03_2026/7ra3_24334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ra3_24334/03_2026/7ra3_24334_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ra3_24334/03_2026/7ra3_24334_neut.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'GLU:plan': 1}
          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: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1}
          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, 'ASP:plan': 2, 'ARG:plan': 1}
          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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 2}
          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: 2.39, per 1000 atoms: 0.22
  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: 0.80
  Conformation dependent library (CDL) restraints added in 525.0 milliseconds
  

  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: 0.28
  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: 1.69

  Time building geometry restraints manager: 1.12 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:             7.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     10.910
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.280
-------------------------------------------------------------------------------
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 : 7.04
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.033   0.001   ARG A 283 
 TYR   0.055   0.002   TYR B  59 
 PHE   0.033   0.002   PHE P   6 
 TRP   0.057   0.002   TRP E 111 
 HIS   0.019   0.002   HIS A 357 

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

*********************** 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  : 0.467 
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: 0.8614 (m110)
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: 0.1128
  time to fit residues: 33.1029
Evaluate side-chains
  160 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
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 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0010
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5526

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

Flipped N/Q/H residues before XYZ refinement:
** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 130 GLN
E 171 GLN
G  11 GLN
P  29 GLN
R 230 ASN
R 242 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.096591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.076530 restraints weight = 33830.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 3.06
r_work: 0.3350 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3353
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3353 r_free = 0.3353    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  11048  Z= 0.126
  Angle     :  0.695  11.075  14991  Z= 0.350
  Chirality :  0.044   0.152   1667
  Planarity :  0.004   0.057   1909
  Dihedral  :  5.192  35.892   1515
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.58 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.23), residues: 1349
  helix:  0.08 (0.24), residues: 429
  sheet: -1.30 (0.27), residues: 340
  loop : -1.18 (0.28), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 283 
 TYR   0.024   0.002   TYR R 259 
 PHE   0.016   0.001   PHE A 212 
 TRP   0.014   0.001   TRP E 111 
 HIS   0.005   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11040)
  covalent geometry    : angle       0.68791 (14975)
  SS BOND              : bond        0.00313 (    8)
  SS BOND              : angle       3.01197 (   16)
  hydrogen bonds       : bond        0.03898 (  518)
  hydrogen bonds       : angle       5.39010 ( 1431)

*********************** 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
  226 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 206
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  262 MET cc_start: 0.7843 (ttm) cc_final: 0.7575 (ttt)
REVERT: E  151 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8309 (ptpt)
REVERT: G   36 ASP cc_start: 0.8048 (m-30) cc_final: 0.7823 (t70)
REVERT: G   47 GLU cc_start: 0.8249 (pt0) cc_final: 0.7989 (pm20)
REVERT: N   18 LEU cc_start: 0.7587 (mt) cc_final: 0.7154 (mt)
REVERT: N   29 PHE cc_start: 0.8821 (t80) cc_final: 0.8586 (t80)
REVERT: N   68 PHE cc_start: 0.8616 (m-80) cc_final: 0.8266 (m-80)
REVERT: N   69 THR cc_start: 0.8517 (m) cc_final: 0.8236 (t)
REVERT: N  123 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8302 (tm-30)
REVERT: P   24 ASN cc_start: 0.8993 (m110) cc_final: 0.8563 (m-40)
REVERT: R  237 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8262 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 219
  average time/residue: 0.0980
  time to fit residues: 30.6763
Evaluate side-chains
  178 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 169
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  318 LEU
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  153 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 101 optimal weight:   30.0000
   chunk 82 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 171 GLN
** G  11 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 = 0.3797 r_free = 0.3797 target = 0.093214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.072645 restraints weight = 34292.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 3.04
r_work: 0.3264 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3266
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3266 r_free = 0.3266    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.34   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 = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3266
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11048  Z= 0.211
  Angle     :  0.710  10.923  14991  Z= 0.363
  Chirality :  0.045   0.202   1667
  Planarity :  0.005   0.054   1909
  Dihedral  :  5.059  36.243   1514
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.42 %
    Favored  : 82.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.23), residues: 1349
  helix:  0.15 (0.24), residues: 435
  sheet: -1.32 (0.27), residues: 342
  loop : -1.34 (0.27), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG N  72 
 TYR   0.024   0.002   TYR R 259 
 PHE   0.016   0.002   PHE A 212 
 TRP   0.019   0.002   TRP R 233 
 HIS   0.007   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (11040)
  covalent geometry    : angle       0.70302 (14975)
  SS BOND              : bond        0.00376 (    8)
  SS BOND              : angle       3.14531 (   16)
  hydrogen bonds       : bond        0.03968 (  518)
  hydrogen bonds       : angle       5.17043 ( 1431)

*********************** 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
  217 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 177
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  198 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8637 (pp)
REVERT: B  210 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8484 (tp)
REVERT: G   36 ASP cc_start: 0.8143 (m-30) cc_final: 0.7873 (t70)
REVERT: N   11 LEU cc_start: 0.8645 (mt) cc_final: 0.8372 (mp)
REVERT: N   69 THR cc_start: 0.8545 (m) cc_final: 0.8188 (p)
REVERT: P   14 MET cc_start: 0.8173 (mmm) cc_final: 0.7930 (mmm)
REVERT: P   18 HIS cc_start: 0.7873 (m-70) cc_final: 0.7617 (m170)
REVERT: P   24 ASN cc_start: 0.9031 (m110) cc_final: 0.8656 (m-40)
REVERT: R  165 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6751 (pp)
REVERT: R  237 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8329 (tm-30)
  outliers start: 40
  outliers final: 21
  residues processed: 205
  average time/residue: 0.0932
  time to fit residues: 28.0197
Evaluate side-chains
  187 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 163
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  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  180 MET
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0020
   chunk 102 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 122 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.9194

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

Flipped N/Q/H residues before XYZ refinement:
** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 384 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.093723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.073281 restraints weight = 34407.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.04
r_work: 0.3277 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
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 = 0.28   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 = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11048  Z= 0.170
  Angle     :  0.683   9.763  14991  Z= 0.347
  Chirality :  0.044   0.200   1667
  Planarity :  0.004   0.053   1909
  Dihedral  :  4.908  37.158   1514
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.97 %
    Favored  : 79.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.23), residues: 1349
  helix:  0.29 (0.25), residues: 437
  sheet: -1.24 (0.27), residues: 339
  loop : -1.36 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.021   0.002   TYR R 259 
 PHE   0.017   0.001   PHE A 212 
 TRP   0.018   0.002   TRP E 111 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (11040)
  covalent geometry    : angle       0.67616 (14975)
  SS BOND              : bond        0.00463 (    8)
  SS BOND              : angle       2.96267 (   16)
  hydrogen bonds       : bond        0.03798 (  518)
  hydrogen bonds       : angle       5.02500 ( 1431)

*********************** 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
  220 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.8028 (p0) cc_final: 0.6882 (t70)
REVERT: B  198 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8567 (pp)
REVERT: B  210 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8455 (tp)
REVERT: B  280 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8312 (ttmm)
REVERT: G   14 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8833 (mtmm)
REVERT: G   20 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8359 (ptpp)
REVERT: G   36 ASP cc_start: 0.8055 (m-30) cc_final: 0.7843 (t70)
REVERT: N   11 LEU cc_start: 0.8623 (mt) cc_final: 0.8408 (mp)
REVERT: N   69 THR cc_start: 0.8531 (m) cc_final: 0.8258 (p)
REVERT: P   24 ASN cc_start: 0.9031 (m110) cc_final: 0.8651 (m110)
REVERT: R  165 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6737 (pp)
REVERT: R  237 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8411 (tm-30)
  outliers start: 43
  outliers final: 25
  residues processed: 206
  average time/residue: 0.0877
  time to fit residues: 26.5838
Evaluate side-chains
  192 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
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   78 LYS
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   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 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  360 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.094287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073962 restraints weight = 33999.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 3.06
r_work: 0.3292 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3295
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3295 r_free = 0.3295    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3295
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11048  Z= 0.149
  Angle     :  0.672   8.449  14991  Z= 0.340
  Chirality :  0.043   0.221   1667
  Planarity :  0.004   0.052   1909
  Dihedral  :  4.756  35.667   1514
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 18.91 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.23), residues: 1349
  helix:  0.46 (0.25), residues: 437
  sheet: -1.13 (0.28), residues: 338
  loop : -1.34 (0.27), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  72 
 TYR   0.020   0.002   TYR R 259 
 PHE   0.021   0.001   PHE P   6 
 TRP   0.014   0.001   TRP E 111 
 HIS   0.005   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (11040)
  covalent geometry    : angle       0.66659 (14975)
  SS BOND              : bond        0.00306 (    8)
  SS BOND              : angle       2.71133 (   16)
  hydrogen bonds       : bond        0.03645 (  518)
  hydrogen bonds       : angle       4.91304 ( 1431)

*********************** 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
  240 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 188
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.8016 (p0) cc_final: 0.6798 (t70)
REVERT: B  210 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8409 (tp)
REVERT: B  280 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8280 (ttmm)
REVERT: G   36 ASP cc_start: 0.8150 (m-30) cc_final: 0.7856 (t70)
REVERT: N   69 THR cc_start: 0.8553 (m) cc_final: 0.8298 (p)
REVERT: P   24 ASN cc_start: 0.9055 (m110) cc_final: 0.8659 (m110)
REVERT: R  165 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6700 (pp)
  outliers start: 52
  outliers final: 32
  residues processed: 223
  average time/residue: 0.0900
  time to fit residues: 29.2214
Evaluate side-chains
  207 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 173
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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   59 TYR
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   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
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 76 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 61 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 87 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    2.0586

-------------------------------------------------------------------------------
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**
N   1 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.093712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.073297 restraints weight = 34013.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.06
r_work: 0.3279 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3280
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3280 r_free = 0.3280    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3280
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11048  Z= 0.177
  Angle     :  0.687   8.462  14991  Z= 0.347
  Chirality :  0.044   0.172   1667
  Planarity :  0.004   0.051   1909
  Dihedral  :  4.768  33.921   1514
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 19.00 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.23), residues: 1349
  helix:  0.45 (0.25), residues: 436
  sheet: -1.07 (0.28), residues: 327
  loop : -1.35 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B   8 
 TYR   0.021   0.002   TYR R 259 
 PHE   0.017   0.002   PHE P   6 
 TRP   0.016   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (11040)
  covalent geometry    : angle       0.68222 (14975)
  SS BOND              : bond        0.00330 (    8)
  SS BOND              : angle       2.62985 (   16)
  hydrogen bonds       : bond        0.03696 (  518)
  hydrogen bonds       : angle       4.90574 ( 1431)

*********************** 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: 56
    poor density    : 183
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9138 (mtpp) cc_final: 0.8873 (mtpp)
REVERT: A  295 ASP cc_start: 0.7914 (p0) cc_final: 0.6862 (t70)
REVERT: B  210 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8445 (tp)
REVERT: B  280 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8332 (ttmm)
REVERT: G   36 ASP cc_start: 0.8203 (m-30) cc_final: 0.7871 (t70)
REVERT: N   69 THR cc_start: 0.8600 (m) cc_final: 0.8357 (p)
REVERT: P    1 TYR cc_start: 0.8107 (p90) cc_final: 0.7836 (p90)
REVERT: P   24 ASN cc_start: 0.9063 (m110) cc_final: 0.8694 (m110)
REVERT: R  165 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6795 (pp)
  outliers start: 56
  outliers final: 38
  residues processed: 219
  average time/residue: 0.0912
  time to fit residues: 29.2542
Evaluate side-chains
  210 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 170
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  302 LEU
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   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   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain G residue    8 SER
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   81 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 123 optimal weight:    8.9990
   chunk 105 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 68 optimal weight:    8.9990
   chunk 39 optimal weight:    0.6980
   chunk 122 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    3.3388

-------------------------------------------------------------------------------
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**
E 219 GLN
E 220 HIS
** G  11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.091877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.071320 restraints weight = 33938.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 3.03
r_work: 0.3233 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3234
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3234 r_free = 0.3234    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3234
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11048  Z= 0.257
  Angle     :  0.755   8.933  14991  Z= 0.385
  Chirality :  0.046   0.176   1667
  Planarity :  0.005   0.057   1909
  Dihedral  :  5.048  34.079   1514
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 19.79 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.23), residues: 1349
  helix:  0.33 (0.25), residues: 431
  sheet: -1.15 (0.28), residues: 338
  loop : -1.35 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B   8 
 TYR   0.022   0.002   TYR R 259 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.019   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (11040)
  covalent geometry    : angle       0.74957 (14975)
  SS BOND              : bond        0.00417 (    8)
  SS BOND              : angle       2.82398 (   16)
  hydrogen bonds       : bond        0.04006 (  518)
  hydrogen bonds       : angle       5.09530 ( 1431)

*********************** 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
  234 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 176
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8914 (mtpp)
REVERT: B  210 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8484 (tp)
REVERT: B  280 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8407 (ttmm)
REVERT: G   36 ASP cc_start: 0.8300 (m-30) cc_final: 0.7938 (t70)
REVERT: G   47 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8048 (mt-10)
REVERT: N   69 THR cc_start: 0.8640 (m) cc_final: 0.8383 (p)
REVERT: P    1 TYR cc_start: 0.8225 (p90) cc_final: 0.8008 (p90)
REVERT: P   15 ASP cc_start: 0.9135 (t70) cc_final: 0.8906 (t0)
REVERT: P   24 ASN cc_start: 0.9078 (m110) cc_final: 0.8713 (m110)
REVERT: R  165 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6749 (pp)
  outliers start: 58
  outliers final: 44
  residues processed: 214
  average time/residue: 0.0939
  time to fit residues: 29.2590
Evaluate side-chains
  211 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 165
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
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  105 TYR
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   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain G residue    8 SER
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 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 P residue   17 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
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 125 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 94 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 219 GLN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.096307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.076363 restraints weight = 33681.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.03
r_work: 0.3347 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11048  Z= 0.122
  Angle     :  0.692   9.745  14991  Z= 0.341
  Chirality :  0.043   0.191   1667
  Planarity :  0.004   0.049   1909
  Dihedral  :  4.620  32.881   1514
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.23), residues: 1349
  helix:  0.60 (0.25), residues: 436
  sheet: -0.78 (0.31), residues: 291
  loop : -1.26 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.017   0.001   TYR R 259 
 PHE   0.018   0.001   PHE A 212 
 TRP   0.020   0.001   TRP B 339 
 HIS   0.004   0.001   HIS A 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11040)
  covalent geometry    : angle       0.68724 (14975)
  SS BOND              : bond        0.00297 (    8)
  SS BOND              : angle       2.52964 (   16)
  hydrogen bonds       : bond        0.03519 (  518)
  hydrogen bonds       : angle       4.80594 ( 1431)

*********************** 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
  236 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 202
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8845 (mtpp)
REVERT: A  295 ASP cc_start: 0.7788 (p0) cc_final: 0.6636 (t70)
REVERT: B  210 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (tp)
REVERT: G   36 ASP cc_start: 0.8186 (m-30) cc_final: 0.7843 (t70)
REVERT: G   47 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7854 (mt-10)
REVERT: N   69 THR cc_start: 0.8563 (m) cc_final: 0.8330 (p)
REVERT: P   15 ASP cc_start: 0.8918 (t70) cc_final: 0.8479 (t70)
REVERT: P   24 ASN cc_start: 0.9073 (m110) cc_final: 0.8720 (m-40)
REVERT: R  259 TYR cc_start: 0.7989 (p90) cc_final: 0.7730 (p90)
REVERT: R  322 LEU cc_start: 0.8565 (tt) cc_final: 0.8039 (tp)
  outliers start: 34
  outliers final: 24
  residues processed: 222
  average time/residue: 0.0912
  time to fit residues: 29.4884
Evaluate side-chains
  203 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  287 VAL
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   59 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  143 VAL
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue  141 TYR
Chi-restraints excluded: chain R residue  153 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 98 optimal weight:    8.9990
   chunk 131 optimal weight:    3.9990
   chunk 114 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 133 optimal weight:    5.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
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 219 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 = 0.3806 r_free = 0.3806 target = 0.093770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.073375 restraints weight = 33944.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 3.07
r_work: 0.3278 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11048  Z= 0.185
  Angle     :  0.744  11.659  14991  Z= 0.368
  Chirality :  0.045   0.201   1667
  Planarity :  0.004   0.050   1909
  Dihedral  :  4.791  31.659   1514
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.81 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.24), residues: 1349
  helix:  0.66 (0.25), residues: 434
  sheet: -0.89 (0.30), residues: 299
  loop : -1.22 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.021   0.002   TYR R 259 
 PHE   0.019   0.002   PHE A 212 
 TRP   0.017   0.002   TRP E 111 
 HIS   0.006   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11040)
  covalent geometry    : angle       0.74011 (14975)
  SS BOND              : bond        0.00345 (    8)
  SS BOND              : angle       2.41273 (   16)
  hydrogen bonds       : bond        0.03676 (  518)
  hydrogen bonds       : angle       4.82357 ( 1431)

*********************** 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
  213 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 171
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.7920 (pt0) cc_final: 0.7539 (tt0)
REVERT: E   93 MET cc_start: 0.8261 (tpt) cc_final: 0.8051 (tpt)
REVERT: G   36 ASP cc_start: 0.8270 (m-30) cc_final: 0.7891 (t70)
REVERT: G   47 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7980 (mt-10)
REVERT: N   69 THR cc_start: 0.8591 (m) cc_final: 0.8337 (p)
REVERT: P   15 ASP cc_start: 0.8949 (t70) cc_final: 0.8488 (t70)
REVERT: P   24 ASN cc_start: 0.9067 (m110) cc_final: 0.8729 (m-40)
REVERT: R  165 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6786 (pp)
REVERT: R  405 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5868 (ttp80)
  outliers start: 42
  outliers final: 32
  residues processed: 198
  average time/residue: 0.0915
  time to fit residues: 26.7746
Evaluate side-chains
  197 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 163
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
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  275 SER
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  143 VAL
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 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  244 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 99 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 102 optimal weight:    6.9990
   chunk 90 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 278 ASN
A 279 ASN
** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3764 r_free = 0.3764 target = 0.091466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.070919 restraints weight = 34299.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 3.05
r_work: 0.3222 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3224
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3224 r_free = 0.3224    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3224
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11048  Z= 0.283
  Angle     :  0.822  10.862  14991  Z= 0.412
  Chirality :  0.048   0.254   1667
  Planarity :  0.005   0.061   1909
  Dihedral  :  5.250  32.858   1514
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.60 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.23), residues: 1349
  helix:  0.47 (0.25), residues: 431
  sheet: -1.06 (0.28), residues: 330
  loop : -1.26 (0.27), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 265 
 TYR   0.022   0.002   TYR R 259 
 PHE   0.019   0.002   PHE A 212 
 TRP   0.025   0.002   TRP R 233 
 HIS   0.007   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00636 (11040)
  covalent geometry    : angle       0.81817 (14975)
  SS BOND              : bond        0.00472 (    8)
  SS BOND              : angle       2.68186 (   16)
  hydrogen bonds       : bond        0.04037 (  518)
  hydrogen bonds       : angle       5.11394 ( 1431)

********************** 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
  199 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 161
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  295 ASP cc_start: 0.7873 (p0) cc_final: 0.6817 (t70)
REVERT: G   36 ASP cc_start: 0.8324 (m-30) cc_final: 0.7916 (t70)
REVERT: N   69 THR cc_start: 0.8604 (m) cc_final: 0.8391 (p)
REVERT: P   15 ASP cc_start: 0.9062 (t70) cc_final: 0.8853 (t0)
REVERT: P   24 ASN cc_start: 0.9097 (m110) cc_final: 0.8770 (m110)
REVERT: R  164 ARG cc_start: 0.6098 (mpt180) cc_final: 0.5827 (mmt-90)
REVERT: R  165 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6861 (pp)
REVERT: R  405 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.5868 (ttp-170)
  outliers start: 38
  outliers final: 33
  residues processed: 186
  average time/residue: 0.0902
  time to fit residues: 24.5893
Evaluate side-chains
  193 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 158
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
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   76 ASP
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  135 VAL
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   84 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain E residue  111 TRP
Chi-restraints excluded: chain E residue  143 VAL
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 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  244 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
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 34 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0980
   chunk 6 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 278 ASN
** B 295 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.095376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.075190 restraints weight = 33884.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 3.08
r_work: 0.3316 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11048  Z= 0.132
  Angle     :  0.740  10.629  14991  Z= 0.362
  Chirality :  0.044   0.290   1667
  Planarity :  0.004   0.049   1909
  Dihedral  :  4.819  31.297   1514
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 23.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.24), residues: 1349
  helix:  0.64 (0.25), residues: 435
  sheet: -0.77 (0.30), residues: 308
  loop : -1.20 (0.27), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 148 
 TYR   0.018   0.002   TYR G  40 
 PHE   0.027   0.001   PHE B 292 
 TRP   0.021   0.002   TRP B 339 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (11040)
  covalent geometry    : angle       0.73597 (14975)
  SS BOND              : bond        0.00346 (    8)
  SS BOND              : angle       2.42973 (   16)
  hydrogen bonds       : bond        0.03546 (  518)
  hydrogen bonds       : angle       4.79886 ( 1431)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.73 seconds
wall clock time: 52 minutes 14.63 seconds (3134.63 seconds total)