Starting phenix.real_space_refine
on Tue Mar  3 23:24:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2026/7vfx_31962.cif"
  }
  resolution = 2.8
  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=   0.004
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    5781      2.51       5
     N    1512      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 9004
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2323
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 12, 'TRANS': 282}
    Chain: "A"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1756
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 38
          Classifications: {'peptide': 4}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 102
          Unusual residues: {'CLR': 3, 'PLM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.16, per 1000 atoms: 0.24
  Number of scatterers: 9004
  At special positions: 0
  Unit cell: (90.1, 124.95, 123.25, 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    1647      8.00
     N    1512      7.00
     C    5781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 0.76
  Conformation dependent library (CDL) restraints added in 387.5 milliseconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.9% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'R' and resid 22 through 54
      removed outlier: 3.610A  pdb=" N   ASP R  26 " --> pdb=" O   TYR R  22 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 76
    Processing helix  chain 'R' and resid 77 through 87
      removed outlier: 3.853A  pdb=" N   PHE R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 146
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 4.459A  pdb=" N   TRP R 150 " --> pdb=" O   ILE R 146 " (cutoff:3.500A)
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 209
      removed outlier: 3.825A  pdb=" N   ARG R 190 " --> pdb=" O   ASP R 186 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ASN R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 236 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 273
      removed outlier: 4.193A  pdb=" N   GLN R 273 " --> pdb=" O   ARG R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 303
      removed outlier: 4.218A  pdb=" N   ALA R 288 " --> pdb=" O   ASP R 284 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU R 289 " --> pdb=" O   VAL R 285 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   SER R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   CYS R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 315
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.000A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.811A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.537A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.552A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.612A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 4.181A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.693A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.890A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 169
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.990A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.179A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.906A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.894A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.738A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.956A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.499A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.727A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.126A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.126A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195
      removed outlier: 6.607A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1287 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: 1.35

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2864
        1.34 -     1.46: 2238
        1.46 -     1.58: 4003
        1.58 -     1.70: 0
        1.70 -     1.82: 95
  Bond restraints: 9200
  Sorted by residual:
  bond pdb=" SD  FME C   1 "
       pdb=" CE  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.750  0.055 2.00e-02 2.50e+03 7.58e+00
  bond pdb=" CG  FME C   1 "
       pdb=" SD  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.771  0.046 2.00e-02 2.50e+03 5.35e+00
  bond pdb=" N   FME C   1 "
       pdb=" CN  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.374 -0.039 2.00e-02 2.50e+03 3.88e+00
  bond pdb=" CA  GLN B  75 "
       pdb=" C   GLN B  75 "
    ideal  model  delta    sigma   weight residual
    1.522  1.490  0.032 1.72e-02 3.38e+03 3.45e+00
  bond pdb=" C10 CLR R 402 "
       pdb=" C9  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.551  1.517  0.034 2.00e-02 2.50e+03 2.91e+00
  ... (remaining 9195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 12159
        1.70 -     3.39: 238
        3.39 -     5.09: 60
        5.09 -     6.78: 13
        6.78 -     8.48: 1
  Bond angle restraints: 12471
  Sorted by residual:
  angle pdb=" N   VAL S  64 "
        pdb=" CA  VAL S  64 "
        pdb=" C   VAL S  64 "
      ideal   model   delta    sigma   weight residual
     113.20  109.73    3.47 9.60e-01 1.09e+00 1.30e+01
  angle pdb=" CB  MET R 197 "
        pdb=" CG  MET R 197 "
        pdb=" SD  MET R 197 "
      ideal   model   delta    sigma   weight residual
     112.70  121.18   -8.48 3.00e+00 1.11e-01 7.98e+00
  angle pdb=" CA  VAL R 302 "
        pdb=" C   VAL R 302 "
        pdb=" N   PHE R 303 "
      ideal   model   delta    sigma   weight residual
     116.60  120.42   -3.82 1.45e+00 4.76e-01 6.94e+00
  angle pdb=" CA  CYS S  96 "
        pdb=" CB  CYS S  96 "
        pdb=" SG  CYS S  96 "
      ideal   model   delta    sigma   weight residual
     114.40  120.19   -5.79 2.30e+00 1.89e-01 6.33e+00
  angle pdb=" C   MET A 240 "
        pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
      ideal   model   delta    sigma   weight residual
     121.54  126.34   -4.80 1.91e+00 2.74e-01 6.32e+00
  ... (remaining 12466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 5263
       24.42 -    48.83: 275
       48.83 -    73.25: 34
       73.25 -    97.67: 12
       97.67 -   122.08: 1
  Dihedral angle restraints: 5585
    sinusoidal: 2300
      harmonic: 3285
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLN S 142 "
           pdb=" C   GLN S 142 "
           pdb=" N   ALA S 143 "
           pdb=" CA  ALA S 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.31  -20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" C10 CLR R 403 "
           pdb=" C1  CLR R 403 "
           pdb=" C2  CLR R 403 "
           pdb=" C3  CLR R 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   65.25 -122.08     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 5582 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 992
       0.042 -    0.084: 324
       0.084 -    0.127: 94
       0.127 -    0.169: 12
       0.169 -    0.211: 7
  Chirality restraints: 1429
  Sorted by residual:
  chirality pdb=" C13 CLR R 403 "
            pdb=" C12 CLR R 403 "
            pdb=" C14 CLR R 403 "
            pdb=" C17 CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.74   -0.19 2.00e-01 2.50e+01 9.50e-01
  chirality pdb=" C13 CLR R 401 "
            pdb=" C12 CLR R 401 "
            pdb=" C14 CLR R 401 "
            pdb=" C17 CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.75   -0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 1426 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 147 "    0.062 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO S 148 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO S 148 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO S 148 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 194 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 158 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO R 159 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO R 159 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 159 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1355
        2.76 -     3.29: 8272
        3.29 -     3.83: 14381
        3.83 -     4.36: 17237
        4.36 -     4.90: 30477
  Nonbonded interactions: 71722
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OD2 ASP B 153 "
            pdb=" NE2 GLN B 156 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" ND2 ASN B 340 "
            pdb=" OD1 ASN G  59 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   GLY S 112 "
            pdb=" OG  SER S 184 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" NZ  LYS S 163 "
            pdb=" OE2 GLU S 234 "
     model   vdw
     2.336 3.120
  ... (remaining 71717 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
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      :  0.003   0.055   9203  Z= 0.168
  Angle     :  0.655   8.477  12477  Z= 0.352
  Chirality :  0.046   0.211   1429
  Planarity :  0.004   0.094   1552
  Dihedral  : 15.033 122.082   3456
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.41 (0.25), residues: 1120
  helix:  1.62 (0.27), residues: 400
  sheet:  0.28 (0.30), residues: 287
  loop : -0.99 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 242 
 TYR   0.011   0.001   TYR S 190 
 PHE   0.019   0.001   PHE B 199 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9200)
  covalent geometry    : angle       0.65431 (12471)
  SS BOND              : bond        0.00787 (    3)
  SS BOND              : angle       1.49804 (    6)
  hydrogen bonds       : bond        0.12824 (  454)
  hydrogen bonds       : angle       5.49114 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.329 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8230 (m110) cc_final: 0.7988 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.6915
  time to fit residues: 87.5634
Evaluate side-chains
  100 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
R 108 ASN
B 220 GLN
S 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.132079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.089023 restraints weight = 12727.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.36
r_work: 0.2861 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9203  Z= 0.200
  Angle     :  0.638   7.039  12477  Z= 0.338
  Chirality :  0.046   0.142   1429
  Planarity :  0.004   0.042   1552
  Dihedral  :  7.636  59.520   1436
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  7.53 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.25), residues: 1120
  helix:  1.65 (0.26), residues: 402
  sheet:  0.31 (0.30), residues: 288
  loop : -0.96 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  42 
 TYR   0.013   0.002   TYR S 190 
 PHE   0.019   0.002   PHE B 199 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 9200)
  covalent geometry    : angle       0.63661 (12471)
  SS BOND              : bond        0.01116 (    3)
  SS BOND              : angle       1.86413 (    6)
  hydrogen bonds       : bond        0.05788 (  454)
  hydrogen bonds       : angle       4.92342 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7087 (mtp180)
REVERT: A  287 TYR cc_start: 0.7673 (m-80) cc_final: 0.7391 (m-80)
REVERT: G   19 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5305 (mp)
REVERT: S   80 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7569 (p90)
REVERT: S  234 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8235 (mt-10)
  outliers start: 15
  outliers final: 0
  residues processed: 111
  average time/residue: 0.6745
  time to fit residues: 79.1217
Evaluate side-chains
  104 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:   20.0000
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
R 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.133489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.089585 restraints weight = 12668.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 2.14
r_work: 0.2914 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9203  Z= 0.139
  Angle     :  0.555   5.859  12477  Z= 0.298
  Chirality :  0.043   0.138   1429
  Planarity :  0.004   0.037   1552
  Dihedral  :  6.745  56.707   1436
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 10.21 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.56 (0.25), residues: 1120
  helix:  1.76 (0.26), residues: 409
  sheet:  0.35 (0.30), residues: 293
  loop : -0.98 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  42 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.015   0.001   PHE A 189 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9200)
  covalent geometry    : angle       0.55380 (12471)
  SS BOND              : bond        0.00838 (    3)
  SS BOND              : angle       1.43686 (    6)
  hydrogen bonds       : bond        0.05014 (  454)
  hydrogen bonds       : angle       4.67606 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7099 (mtp180)
REVERT: A  287 TYR cc_start: 0.7687 (m-80) cc_final: 0.7394 (m-80)
REVERT: B  217 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6937 (pp-130)
REVERT: G   19 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5154 (mp)
REVERT: S  234 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (mt-10)
  outliers start: 14
  outliers final: 3
  residues processed: 112
  average time/residue: 0.6312
  time to fit residues: 74.8556
Evaluate side-chains
  109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 52 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 62 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   chunk 87 optimal weight:    0.0010
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    3.1994

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.088538 restraints weight = 12859.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 2.30
r_work: 0.2869 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9203  Z= 0.200
  Angle     :  0.610   6.717  12477  Z= 0.327
  Chirality :  0.045   0.143   1429
  Planarity :  0.004   0.039   1552
  Dihedral  :  6.860  56.749   1436
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.86 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.50 (0.25), residues: 1120
  helix:  1.66 (0.26), residues: 409
  sheet:  0.30 (0.30), residues: 297
  loop : -0.96 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 197 
 TYR   0.011   0.002   TYR S 190 
 PHE   0.019   0.002   PHE B 199 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9200)
  covalent geometry    : angle       0.60864 (12471)
  SS BOND              : bond        0.01059 (    3)
  SS BOND              : angle       1.74489 (    6)
  hydrogen bonds       : bond        0.05700 (  454)
  hydrogen bonds       : angle       4.79727 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7137 (mtp180)
REVERT: A  287 TYR cc_start: 0.7576 (m-80) cc_final: 0.7206 (m-80)
REVERT: A  318 GLU cc_start: 0.8106 (tt0) cc_final: 0.7562 (mm-30)
REVERT: G   19 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5234 (mp)
REVERT: S  234 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8192 (mt-10)
  outliers start: 18
  outliers final: 7
  residues processed: 108
  average time/residue: 0.6521
  time to fit residues: 74.5049
Evaluate side-chains
  110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.132940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.089005 restraints weight = 12772.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.18
r_work: 0.2906 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9203  Z= 0.144
  Angle     :  0.553   6.751  12477  Z= 0.297
  Chirality :  0.043   0.138   1429
  Planarity :  0.003   0.037   1552
  Dihedral  :  6.519  55.965   1436
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.78 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.62 (0.25), residues: 1120
  helix:  1.79 (0.26), residues: 409
  sheet:  0.42 (0.30), residues: 292
  loop : -0.98 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  42 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS R  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9200)
  covalent geometry    : angle       0.55262 (12471)
  SS BOND              : bond        0.00846 (    3)
  SS BOND              : angle       1.37944 (    6)
  hydrogen bonds       : bond        0.04983 (  454)
  hydrogen bonds       : angle       4.61883 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7092 (mtp180)
REVERT: A  287 TYR cc_start: 0.7585 (m-80) cc_final: 0.7208 (m-80)
REVERT: A  311 ASN cc_start: 0.8604 (t0) cc_final: 0.8199 (t0)
REVERT: A  318 GLU cc_start: 0.8125 (tt0) cc_final: 0.7572 (mm-30)
REVERT: B  217 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6990 (pp-130)
REVERT: G   19 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5218 (mp)
REVERT: S  234 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8094 (mt-10)
  outliers start: 17
  outliers final: 7
  residues processed: 112
  average time/residue: 0.6794
  time to fit residues: 80.4294
Evaluate side-chains
  112 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 110 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 54 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.092378 restraints weight = 12761.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 2.14
r_work: 0.2958 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9203  Z= 0.104
  Angle     :  0.508   8.218  12477  Z= 0.271
  Chirality :  0.041   0.133   1429
  Planarity :  0.003   0.034   1552
  Dihedral  :  6.133  57.544   1436
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.81 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.87 (0.25), residues: 1120
  helix:  2.02 (0.26), residues: 409
  sheet:  0.71 (0.31), residues: 267
  loop : -0.89 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.013   0.001   PHE A 189 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 9200)
  covalent geometry    : angle       0.50737 (12471)
  SS BOND              : bond        0.00598 (    3)
  SS BOND              : angle       1.05582 (    6)
  hydrogen bonds       : bond        0.04196 (  454)
  hydrogen bonds       : angle       4.38830 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.344 
Fit side-chains
REVERT: R  152 MET cc_start: 0.8510 (mtm) cc_final: 0.8204 (mtt)
REVERT: A  287 TYR cc_start: 0.7596 (m-80) cc_final: 0.7293 (m-80)
REVERT: A  311 ASN cc_start: 0.8573 (t0) cc_final: 0.8176 (t0)
REVERT: A  318 GLU cc_start: 0.8111 (tt0) cc_final: 0.7620 (mm-30)
REVERT: B  217 MET cc_start: 0.7384 (ptt) cc_final: 0.7069 (pp-130)
REVERT: G   19 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5267 (mp)
REVERT: S  234 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (mt-10)
REVERT: S  245 LEU cc_start: 0.8769 (tt) cc_final: 0.8506 (tp)
  outliers start: 16
  outliers final: 7
  residues processed: 117
  average time/residue: 0.6183
  time to fit residues: 76.7876
Evaluate side-chains
  113 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 86 optimal weight:    0.0980
   chunk 101 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 88 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 17 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.134108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.090606 restraints weight = 12916.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.15
r_work: 0.2927 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9203  Z= 0.133
  Angle     :  0.538   8.590  12477  Z= 0.288
  Chirality :  0.042   0.138   1429
  Planarity :  0.003   0.035   1552
  Dihedral  :  6.248  56.386   1436
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.23 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.25), residues: 1120
  helix:  2.00 (0.26), residues: 409
  sheet:  0.63 (0.30), residues: 280
  loop : -0.88 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9200)
  covalent geometry    : angle       0.53742 (12471)
  SS BOND              : bond        0.00770 (    3)
  SS BOND              : angle       1.25358 (    6)
  hydrogen bonds       : bond        0.04702 (  454)
  hydrogen bonds       : angle       4.46751 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7065 (mtp180)
REVERT: A  287 TYR cc_start: 0.7660 (m-80) cc_final: 0.7268 (m-80)
REVERT: A  311 ASN cc_start: 0.8605 (t0) cc_final: 0.8199 (t0)
REVERT: A  318 GLU cc_start: 0.8158 (tt0) cc_final: 0.7660 (mm-30)
REVERT: B  217 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7025 (pp-130)
REVERT: G   19 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5251 (mp)
REVERT: S  234 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8089 (mt-10)
REVERT: S  245 LEU cc_start: 0.8783 (tt) cc_final: 0.8535 (tp)
  outliers start: 17
  outliers final: 10
  residues processed: 115
  average time/residue: 0.6327
  time to fit residues: 77.0960
Evaluate side-chains
  119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0470
   chunk 19 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
R 293 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.093077 restraints weight = 12799.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.28
r_work: 0.2946 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9203  Z= 0.109
  Angle     :  0.511   9.011  12477  Z= 0.273
  Chirality :  0.041   0.133   1429
  Planarity :  0.003   0.034   1552
  Dihedral  :  6.055  56.975   1436
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.95 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.96 (0.25), residues: 1120
  helix:  2.08 (0.26), residues: 409
  sheet:  0.66 (0.31), residues: 274
  loop : -0.78 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9200)
  covalent geometry    : angle       0.51092 (12471)
  SS BOND              : bond        0.00631 (    3)
  SS BOND              : angle       1.04758 (    6)
  hydrogen bonds       : bond        0.04258 (  454)
  hydrogen bonds       : angle       4.34168 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.357 
Fit side-chains
REVERT: R  152 MET cc_start: 0.8507 (mtm) cc_final: 0.8199 (mtt)
REVERT: A  287 TYR cc_start: 0.7590 (m-80) cc_final: 0.7216 (m-80)
REVERT: A  311 ASN cc_start: 0.8571 (t0) cc_final: 0.8209 (t0)
REVERT: A  318 GLU cc_start: 0.8165 (tt0) cc_final: 0.7641 (mm-30)
REVERT: B  217 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7026 (pp-130)
REVERT: G   19 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5270 (mp)
REVERT: S  234 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8035 (mt-10)
REVERT: S  245 LEU cc_start: 0.8778 (tt) cc_final: 0.8532 (tp)
  outliers start: 16
  outliers final: 9
  residues processed: 117
  average time/residue: 0.6137
  time to fit residues: 76.3489
Evaluate side-chains
  118 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 70 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.091510 restraints weight = 12701.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.36
r_work: 0.2909 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9203  Z= 0.134
  Angle     :  0.547   9.216  12477  Z= 0.292
  Chirality :  0.042   0.138   1429
  Planarity :  0.003   0.034   1552
  Dihedral  :  6.172  56.034   1436
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.26 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.92 (0.25), residues: 1120
  helix:  2.01 (0.26), residues: 409
  sheet:  0.62 (0.30), residues: 285
  loop : -0.78 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  27 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9200)
  covalent geometry    : angle       0.54680 (12471)
  SS BOND              : bond        0.00745 (    3)
  SS BOND              : angle       1.22397 (    6)
  hydrogen bonds       : bond        0.04661 (  454)
  hydrogen bonds       : angle       4.42926 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  287 TYR cc_start: 0.7599 (m-80) cc_final: 0.7257 (m-80)
REVERT: A  311 ASN cc_start: 0.8620 (t0) cc_final: 0.8256 (t0)
REVERT: A  318 GLU cc_start: 0.8191 (tt0) cc_final: 0.7673 (mm-30)
REVERT: B  217 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7006 (pp-130)
REVERT: G   19 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5288 (mp)
REVERT: S  234 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8112 (mt-10)
REVERT: S  245 LEU cc_start: 0.8779 (tt) cc_final: 0.8553 (tp)
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.6302
  time to fit residues: 76.3303
Evaluate side-chains
  117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 25 optimal weight:    0.4980
   chunk 97 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0970
   chunk 54 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.137223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.095037 restraints weight = 12738.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.34
r_work: 0.2972 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9203  Z= 0.099
  Angle     :  0.506   9.866  12477  Z= 0.270
  Chirality :  0.041   0.129   1429
  Planarity :  0.003   0.033   1552
  Dihedral  :  5.865  58.133   1436
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.46 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.09 (0.25), residues: 1120
  helix:  2.15 (0.26), residues: 409
  sheet:  0.82 (0.31), residues: 271
  loop : -0.71 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  27 
 TYR   0.012   0.001   TYR S 190 
 PHE   0.012   0.001   PHE R 308 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.002   0.000   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 9200)
  covalent geometry    : angle       0.50579 (12471)
  SS BOND              : bond        0.00493 (    3)
  SS BOND              : angle       0.84429 (    6)
  hydrogen bonds       : bond        0.03850 (  454)
  hydrogen bonds       : angle       4.19531 ( 1287)

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.230 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8212 (m110) cc_final: 0.7928 (m110)
REVERT: A  287 TYR cc_start: 0.7562 (m-80) cc_final: 0.7204 (m-80)
REVERT: A  311 ASN cc_start: 0.8557 (t0) cc_final: 0.8261 (t0)
REVERT: A  318 GLU cc_start: 0.8142 (tt0) cc_final: 0.7652 (mm-30)
REVERT: B   42 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.7425 (tmm-80)
REVERT: B  217 MET cc_start: 0.7385 (ptt) cc_final: 0.7052 (pp-130)
REVERT: B  262 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8414 (mtp)
REVERT: G   19 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5146 (mp)
REVERT: S  219 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8085 (tt)
REVERT: S  234 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7926 (mt-10)
REVERT: S  245 LEU cc_start: 0.8788 (tt) cc_final: 0.8586 (tp)
  outliers start: 12
  outliers final: 6
  residues processed: 115
  average time/residue: 0.6055
  time to fit residues: 74.0070
Evaluate side-chains
  117 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  219 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    9.9990
   chunk 80 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 93 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0070
   chunk 70 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    3.6006

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.087576 restraints weight = 12601.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.14
r_work: 0.2882 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9203  Z= 0.219
  Angle     :  0.631   9.780  12477  Z= 0.336
  Chirality :  0.046   0.142   1429
  Planarity :  0.004   0.034   1552
  Dihedral  :  6.568  56.350   1436
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.77 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.81 (0.25), residues: 1120
  helix:  1.83 (0.26), residues: 410
  sheet:  0.64 (0.30), residues: 282
  loop : -0.78 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG G  27 
 TYR   0.012   0.002   TYR A 320 
 PHE   0.021   0.002   PHE A 189 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 9200)
  covalent geometry    : angle       0.63018 (12471)
  SS BOND              : bond        0.01048 (    3)
  SS BOND              : angle       1.69371 (    6)
  hydrogen bonds       : bond        0.05640 (  454)
  hydrogen bonds       : angle       4.64472 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3921.82 seconds
wall clock time: 67 minutes 14.81 seconds (4034.81 seconds total)