Starting phenix.real_space_refine
on Tue Aug  4 20:40:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uns_42415/08_2026/8uns_42415.map"
  }
  resolution = 3.4
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      42      5.16       5
     C    4291      2.51       5
     N    1154      2.21       5
     O    1193      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6683
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1788
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 242, 1776
          Classifications: {'peptide': 242}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 296
          Unresolved non-hydrogen dihedrals: 195
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'ASN:plan1': 3, 'GLU:plan': 15, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 171
      Conformer: "B"
        Number of residues, atoms: 242, 1776
          Classifications: {'peptide': 242}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 296
          Unresolved non-hydrogen dihedrals: 195
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 10, 'ASN:plan1': 3, 'GLU:plan': 15, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 171
          bond proxies already assigned to first conformer: 1797
    Chain: "B"
      Number of atoms: 2364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2364
          Classifications: {'peptide': 329}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 5, 'TRANS': 323}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 163
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 126
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 5, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 13}
          Unresolved non-hydrogen planarities: 131
    Chain: "G"
      Number of atoms: 373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 373
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "R"
      Number of atoms: 2110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2110
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 59}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 205
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 9, 'TRP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 109
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 1.72, per 1000 atoms: 0.26
  Number of scatterers: 6683
  At special positions: 0
  Unit cell: (83.2992, 137.097, 98.9178, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       3     15.00
     O    1193      8.00
     N    1154      7.00
     C    4291      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " 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: 0.58
  Conformation dependent library (CDL) restraints added in 545.2 milliseconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      47.2% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 4.050A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.646A  pdb=" N   ARG A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ILE A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 4.005A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
      removed outlier: 3.555A  pdb=" N   GLU A 268 " --> pdb=" O   ASN A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.537A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.154A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.671A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.673A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 3.627A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.552A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 6 through 22
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.586A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.546A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 68 through 97
      removed outlier: 4.356A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 120
    Processing helix  chain 'R' and resid 121 through 137
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 164
      removed outlier: 3.624A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
      removed outlier: 3.623A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.568A  pdb=" N   ALA R 200 " --> pdb=" O   ASN R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.742A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 3.909A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.846A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.514A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
      removed outlier: 3.510A  pdb=" N   CYS R 327 " --> pdb=" O   PRO R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 329 through 339
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 7.201A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.670A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.010A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.566A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.376A  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 151
      removed outlier: 7.013A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.842A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 6.897A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.853A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1047 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: 1.15

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1596
        1.33 -     1.45: 1497
        1.45 -     1.58: 3674
        1.58 -     1.70: 5
        1.70 -     1.82: 57
  Bond restraints: 6829
  Sorted by residual:
  bond pdb=" N   ILE A 257 "
       pdb=" CA  ILE A 257 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.046 1.14e-02 7.69e+03 1.61e+01
  bond pdb=" N   VAL A 256 "
       pdb=" CA  VAL A 256 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.32e-02 5.74e+03 1.03e+01
  bond pdb=" CA  ASP A 223 "
       pdb=" C   ASP A 223 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.037 1.19e-02 7.06e+03 9.50e+00
  bond pdb=" N   ARG A  61 "
       pdb=" CA  ARG A  61 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.61e+00
  bond pdb=" N   ILE A  62 "
       pdb=" CA  ILE A  62 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.19e-02 7.06e+03 7.46e+00
  ... (remaining 6824 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 9062
        2.08 -     4.16: 237
        4.16 -     6.24: 35
        6.24 -     8.32: 9
        8.32 -    10.40: 6
  Bond angle restraints: 9349
  Sorted by residual:
  angle pdb=" C   GLN A 262 "
        pdb=" CA  GLN A 262 "
        pdb=" CB  GLN A 262 "
      ideal   model   delta    sigma   weight residual
     116.54  108.64    7.90 1.15e+00 7.56e-01 4.72e+01
  angle pdb=" N   GLU A 259 "
        pdb=" CA  GLU A 259 "
        pdb=" C   GLU A 259 "
      ideal   model   delta    sigma   weight residual
     113.23  105.07    8.16 1.22e+00 6.72e-01 4.47e+01
  angle pdb=" N   GLN A  19 "
        pdb=" CA  GLN A  19 "
        pdb=" C   GLN A  19 "
      ideal   model   delta    sigma   weight residual
     111.28  104.93    6.35 1.09e+00 8.42e-01 3.39e+01
  angle pdb=" N   ASN A 261 "
        pdb=" CA  ASN A 261 "
        pdb=" C   ASN A 261 "
      ideal   model   delta    sigma   weight residual
     111.28  105.61    5.67 1.09e+00 8.42e-01 2.70e+01
  angle pdb=" CA  LEU A  63 "
        pdb=" C   LEU A  63 "
        pdb=" O   LEU A  63 "
      ideal   model   delta    sigma   weight residual
     120.55  115.23    5.32 1.06e+00 8.90e-01 2.52e+01
  ... (remaining 9344 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.23: 3818
       28.23 -    56.46: 112
       56.46 -    84.69: 7
       84.69 -   112.92: 4
      112.92 -   141.15: 4
  Dihedral angle restraints: 3945
    sinusoidal: 1267
      harmonic: 2678
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.31  -60.31     1      1.00e+01 1.00e-02 4.85e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -149.58 -141.15     1      2.00e+01 2.50e-03 4.27e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -28.04  132.64     1      2.00e+01 2.50e-03 4.03e+01
  ... (remaining 3942 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 886
       0.054 -    0.107: 165
       0.107 -    0.161: 53
       0.161 -    0.214: 8
       0.214 -    0.268: 7
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" CA  ASP A 260 "
            pdb=" N   ASP A 260 "
            pdb=" C   ASP A 260 "
            pdb=" CB  ASP A 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  GLN A  19 "
            pdb=" N   GLN A  19 "
            pdb=" C   GLN A  19 "
            pdb=" CB  GLN A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1116 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 210 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO R 211 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.013 2.00e-02 2.50e+03   9.94e-03 1.98e+00
        pdb=" CG  TYR B  59 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  15 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.80e+00
        pdb=" C   GLU A  15 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   GLU A  15 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A  16 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 2367
        2.85 -     3.36: 6024
        3.36 -     3.87: 10280
        3.87 -     4.39: 10938
        4.39 -     4.90: 20361
  Nonbonded interactions: 49970
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OD2 ASP B 258 "
            pdb=" NH2 ARG G  27 "
     model   vdw
     2.368 3.120
  nonbonded pdb=" ND2 ASN B 230 "
            pdb=" OD1 ASP B 246 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.407 3.040
  ... (remaining 49965 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=0.49 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:             3.600
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.450
  Find NCS groups from input model:        0.050
  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:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6831  Z= 0.284
  Angle     :  0.770  10.404   9353  Z= 0.494
  Chirality :  0.051   0.268   1119
  Planarity :  0.003   0.043   1173
  Dihedral  : 14.481 141.151   2201
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  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:  1.05 (0.29), residues: 905
  helix:  2.33 (0.27), residues: 393
  sheet:  0.02 (0.41), residues: 173
  loop : -0.92 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.024   0.001   TYR B  59 
 PHE   0.013   0.001   PHE A 222 
 TRP   0.007   0.001   TRP R 158 
 HIS   0.006   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00441 /  0.28 ( 6829)
  covalent geometry    : angle       0.77052 /  0.49 ( 9349)
  SS BOND              : bond        0.00053 /  0.03 (    2)
  SS BOND              : angle       0.60424 /  0.33 (    4)
  hydrogen bonds       : bond        0.18965 / 13.21 (  361)
  hydrogen bonds       : angle       6.66163 /  4.76 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.254 
Fit side-chains
REVERT: G   15 LEU cc_start: 0.8931 (tp) cc_final: 0.8649 (tp)
REVERT: R  171 MET cc_start: 0.7983 (mmm) cc_final: 0.7769 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0708
  time to fit residues: 9.4921
Evaluate side-chains
  74 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.1332 > 50:)
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.123370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099501 restraints weight = 31919.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 3.96
r_work: 0.3021 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.0999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6831  Z= 0.129
  Angle     :  0.491   5.957   9353  Z= 0.263
  Chirality :  0.041   0.149   1119
  Planarity :  0.003   0.043   1173
  Dihedral  :  9.855 157.714   1006
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.77 %
    Favored  : 91.07 %
  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:  1.27 (0.29), residues: 905
  helix:  2.50 (0.27), residues: 401
  sheet:  0.26 (0.41), residues: 170
  loop : -0.95 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  13 
 TYR   0.024   0.001   TYR B  59 
 PHE   0.015   0.001   PHE A 212 
 TRP   0.011   0.001   TRP B 297 
 HIS   0.003   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 6829)
  covalent geometry    : angle       0.49071 /  0.26 ( 9349)
  SS BOND              : bond        0.00013 /  0.01 (    2)
  SS BOND              : angle       0.49704 /  0.28 (    4)
  hydrogen bonds       : bond        0.04621 /  3.34 (  361)
  hydrogen bonds       : angle       4.34911 /  3.13 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8218 (mmtt)
REVERT: A  267 GLN cc_start: 0.8699 (tp40) cc_final: 0.8389 (tm-30)
REVERT: A  368 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7255 (m-30)
REVERT: R   61 PHE cc_start: 0.8752 (m-80) cc_final: 0.8505 (m-10)
REVERT: R  171 MET cc_start: 0.8056 (mmm) cc_final: 0.7829 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 85
  average time/residue: 0.0740
  time to fit residues: 8.7307
Evaluate side-chains
  82 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 85 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.0584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.123329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098930 restraints weight = 36804.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 4.17
r_work: 0.3007 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6831  Z= 0.123
  Angle     :  0.470   5.880   9353  Z= 0.250
  Chirality :  0.040   0.164   1119
  Planarity :  0.003   0.043   1173
  Dihedral  :  8.206 108.881   1006
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.92 %
    Favored  : 89.09 %
  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:  1.46 (0.29), residues: 905
  helix:  2.76 (0.27), residues: 401
  sheet:  0.08 (0.40), residues: 172
  loop : -0.82 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 137 
 TYR   0.024   0.001   TYR B  59 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.008   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 6829)
  covalent geometry    : angle       0.46965 /  0.25 ( 9349)
  SS BOND              : bond        0.00049 /  0.03 (    2)
  SS BOND              : angle       0.41228 /  0.22 (    4)
  hydrogen bonds       : bond        0.04171 /  3.01 (  361)
  hydrogen bonds       : angle       4.01015 /  2.91 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8178 (mmtt)
REVERT: A  267 GLN cc_start: 0.8772 (tp40) cc_final: 0.8417 (tm-30)
REVERT: A  368 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7299 (m-30)
REVERT: R  171 MET cc_start: 0.7990 (mmm) cc_final: 0.7732 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 89
  average time/residue: 0.0760
  time to fit residues: 9.4982
Evaluate side-chains
  82 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.123997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.099952 restraints weight = 31605.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.92
r_work: 0.3028 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6831  Z= 0.106
  Angle     :  0.453   6.433   9353  Z= 0.239
  Chirality :  0.040   0.153   1119
  Planarity :  0.003   0.042   1173
  Dihedral  :  7.842 102.865   1006
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.57 %
    Favored  : 86.78 %
  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:  1.54 (0.29), residues: 905
  helix:  2.85 (0.27), residues: 400
  sheet:  0.13 (0.40), residues: 171
  loop : -0.82 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 ( 6829)
  covalent geometry    : angle       0.45303 /  0.24 ( 9349)
  SS BOND              : bond        0.00041 /  0.02 (    2)
  SS BOND              : angle       0.37544 /  0.21 (    4)
  hydrogen bonds       : bond        0.03732 /  2.70 (  361)
  hydrogen bonds       : angle       3.86515 /  2.81 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 GLN cc_start: 0.8727 (tp40) cc_final: 0.8334 (tm-30)
REVERT: A  368 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7320 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 93
  average time/residue: 0.0674
  time to fit residues: 8.8192
Evaluate side-chains
  89 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Chi-restraints excluded: chain R residue  339 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 60 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.099813 restraints weight = 29356.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.65
r_work: 0.3040 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6831  Z= 0.102
  Angle     :  0.446   6.300   9353  Z= 0.236
  Chirality :  0.040   0.151   1119
  Planarity :  0.003   0.041   1173
  Dihedral  :  7.602  99.803   1006
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.73 %
    Favored  : 85.29 %
  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:  1.60 (0.30), residues: 905
  helix:  2.91 (0.27), residues: 400
  sheet:  0.15 (0.41), residues: 171
  loop : -0.79 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G  13 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 6829)
  covalent geometry    : angle       0.44619 /  0.24 ( 9349)
  SS BOND              : bond        0.00014 /  0.01 (    2)
  SS BOND              : angle       0.38265 /  0.21 (    4)
  hydrogen bonds       : bond        0.03521 /  2.55 (  361)
  hydrogen bonds       : angle       3.75108 /  2.73 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 GLN cc_start: 0.8955 (mt0) cc_final: 0.8681 (pt0)
REVERT: A  267 GLN cc_start: 0.8790 (tp40) cc_final: 0.8398 (tm-30)
REVERT: A  368 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7284 (m-30)
REVERT: R   61 PHE cc_start: 0.8540 (m-10) cc_final: 0.8339 (m-80)
  outliers start: 12
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0693
  time to fit residues: 9.1959
Evaluate side-chains
  92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain R residue   94 ILE
Chi-restraints excluded: chain R residue   96 THR
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 78 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  23 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.118836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.094639 restraints weight = 38367.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 4.23
r_work: 0.2940 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2942
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2942 r_free = 0.2942    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2942
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   6831  Z= 0.214
  Angle     :  0.547   6.253   9353  Z= 0.292
  Chirality :  0.043   0.159   1119
  Planarity :  0.004   0.045   1173
  Dihedral  :  7.767 100.223   1006
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 13.55 %
    Favored  : 83.31 %
  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:  1.30 (0.29), residues: 905
  helix:  2.59 (0.27), residues: 404
  sheet:  0.02 (0.41), residues: 170
  loop : -0.90 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.015   0.001   TYR A 339 
 PHE   0.015   0.002   PHE B 241 
 TRP   0.008   0.001   TRP B  82 
 HIS   0.008   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00521 /  0.21 ( 6829)
  covalent geometry    : angle       0.54719 /  0.29 ( 9349)
  SS BOND              : bond        0.00134 /  0.07 (    2)
  SS BOND              : angle       0.41031 /  0.21 (    4)
  hydrogen bonds       : bond        0.05262 /  3.77 (  361)
  hydrogen bonds       : angle       4.14527 /  3.00 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8409 (mmtt)
REVERT: A  368 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7437 (m-30)
REVERT: B  234 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.7998 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 90
  average time/residue: 0.0618
  time to fit residues: 7.8614
Evaluate side-chains
  87 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  296 HIS
Chi-restraints excluded: chain R residue  307 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 78 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0030
   overall best weight:    0.7390

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.122989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.098201 restraints weight = 41556.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 4.41
r_work: 0.2990 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6831  Z= 0.102
  Angle     :  0.455   6.373   9353  Z= 0.242
  Chirality :  0.040   0.154   1119
  Planarity :  0.003   0.043   1173
  Dihedral  :  7.450 100.388   1006
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.88 %
    Favored  : 83.31 %
  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:  1.51 (0.30), residues: 905
  helix:  2.80 (0.27), residues: 401
  sheet:  0.16 (0.42), residues: 171
  loop : -0.84 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.014   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.007   0.001   TRP B 297 
 HIS   0.007   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00223 /  0.10 ( 6829)
  covalent geometry    : angle       0.45547 /  0.24 ( 9349)
  SS BOND              : bond        0.00036 /  0.02 (    2)
  SS BOND              : angle       0.39170 /  0.22 (    4)
  hydrogen bonds       : bond        0.03631 /  2.63 (  361)
  hydrogen bonds       : angle       3.80707 /  2.76 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 GLN cc_start: 0.8987 (mt0) cc_final: 0.8683 (pt0)
REVERT: A  267 GLN cc_start: 0.8794 (tp40) cc_final: 0.8391 (tm-30)
REVERT: A  368 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7486 (m-30)
REVERT: B  234 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.7899 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0585
  time to fit residues: 7.8059
Evaluate side-chains
  92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  144 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 41 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.124316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.101903 restraints weight = 19976.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.90
r_work: 0.3102 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6831  Z= 0.091
  Angle     :  0.435   6.188   9353  Z= 0.230
  Chirality :  0.039   0.143   1119
  Planarity :  0.003   0.043   1173
  Dihedral  :  7.225 101.227   1006
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 2.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 15.37 %
    Favored  : 83.14 %
  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:  1.63 (0.30), residues: 905
  helix:  2.94 (0.27), residues: 400
  sheet:  0.22 (0.42), residues: 171
  loop : -0.81 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G  13 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.010   0.001   PHE B 241 
 TRP   0.008   0.001   TRP R 313 
 HIS   0.007   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00193 /  0.09 ( 6829)
  covalent geometry    : angle       0.43535 /  0.23 ( 9349)
  SS BOND              : bond        0.00058 /  0.03 (    2)
  SS BOND              : angle       0.45353 /  0.26 (    4)
  hydrogen bonds       : bond        0.03125 /  2.26 (  361)
  hydrogen bonds       : angle       3.64197 /  2.66 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 GLN cc_start: 0.8913 (mt0) cc_final: 0.8654 (pt0)
REVERT: A  267 GLN cc_start: 0.8777 (tp40) cc_final: 0.8348 (tm-30)
REVERT: A  368 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7312 (m-30)
REVERT: B  234 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.7801 (t80)
  outliers start: 9
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0628
  time to fit residues: 8.4260
Evaluate side-chains
  92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   overall best weight:    1.0382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.122682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.099386 restraints weight = 30437.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 3.77
r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8731
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6831  Z= 0.118
  Angle     :  0.462   6.479   9353  Z= 0.245
  Chirality :  0.040   0.158   1119
  Planarity :  0.003   0.042   1173
  Dihedral  :  7.282 101.458   1006
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.87 %
    Favored  : 82.48 %
  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:  1.61 (0.30), residues: 905
  helix:  2.94 (0.27), residues: 400
  sheet:  0.19 (0.42), residues: 171
  loop : -0.84 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.012   0.001   PHE A 222 
 TRP   0.006   0.001   TRP B 297 
 HIS   0.010   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 6829)
  covalent geometry    : angle       0.46222 /  0.25 ( 9349)
  SS BOND              : bond        0.00023 /  0.01 (    2)
  SS BOND              : angle       0.42352 /  0.24 (    4)
  hydrogen bonds       : bond        0.03616 /  2.60 (  361)
  hydrogen bonds       : angle       3.70836 /  2.70 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 GLN cc_start: 0.8947 (mt0) cc_final: 0.8693 (pt0)
REVERT: A  267 GLN cc_start: 0.8810 (tp40) cc_final: 0.8326 (tm-30)
REVERT: A  368 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7342 (m-30)
REVERT: B   59 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8427 (m-80)
REVERT: B   75 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7421 (mt0)
REVERT: B  234 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.7838 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0610
  time to fit residues: 7.8085
Evaluate side-chains
  91 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0170
   chunk 18 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.5416

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.124718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.100093 restraints weight = 38605.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 4.26
r_work: 0.3022 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3024
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3024 r_free = 0.3024    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6831  Z= 0.089
  Angle     :  0.438   6.224   9353  Z= 0.231
  Chirality :  0.039   0.154   1119
  Planarity :  0.003   0.041   1173
  Dihedral  :  7.179 102.028   1006
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.03 %
    Favored  : 82.31 %
  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:  1.67 (0.30), residues: 905
  helix:  3.00 (0.27), residues: 400
  sheet:  0.21 (0.42), residues: 171
  loop : -0.81 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 342 
 TYR   0.013   0.001   TYR A 339 
 PHE   0.012   0.001   PHE A 222 
 TRP   0.007   0.001   TRP R 313 
 HIS   0.009   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00189 /  0.09 ( 6829)
  covalent geometry    : angle       0.43786 /  0.23 ( 9349)
  SS BOND              : bond        0.00033 /  0.02 (    2)
  SS BOND              : angle       0.42761 /  0.24 (    4)
  hydrogen bonds       : bond        0.03046 /  2.20 (  361)
  hydrogen bonds       : angle       3.60627 /  2.63 ( 1047)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8434 (mmtt)
REVERT: A  236 GLN cc_start: 0.8940 (mt0) cc_final: 0.8682 (pt0)
REVERT: A  267 GLN cc_start: 0.8755 (tp40) cc_final: 0.8287 (tm-30)
REVERT: A  368 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7440 (m-30)
REVERT: B   59 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8279 (m-80)
REVERT: B   75 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7472 (mt0)
REVERT: B  234 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.7843 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 87
  average time/residue: 0.0648
  time to fit residues: 8.2789
Evaluate side-chains
  90 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 ASP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 26 optimal weight:    0.0570
   chunk 82 optimal weight:    0.0070
   chunk 83 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.3916

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.101931 restraints weight = 31873.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.74
r_work: 0.3069 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8674
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6831  Z= 0.082
  Angle     :  0.432   6.298   9353  Z= 0.226
  Chirality :  0.039   0.147   1119
  Planarity :  0.003   0.039   1173
  Dihedral  :  7.048 102.639   1006
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.69 %
    Favored  : 81.98 %
  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:  1.74 (0.30), residues: 905
  helix:  3.07 (0.27), residues: 400
  sheet:  0.18 (0.42), residues: 171
  loop : -0.76 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 347 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 222 
 TRP   0.008   0.001   TRP R 313 
 HIS   0.008   0.001   HIS A 220 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00167 /  0.08 ( 6829)
  covalent geometry    : angle       0.43189 /  0.23 ( 9349)
  SS BOND              : bond        0.00063 /  0.03 (    2)
  SS BOND              : angle       0.48007 /  0.28 (    4)
  hydrogen bonds       : bond        0.02727 /  1.97 (  361)
  hydrogen bonds       : angle       3.50962 /  2.57 ( 1047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1632.88 seconds
wall clock time: 28 minutes 34.38 seconds (1714.38 seconds total)