Starting phenix.real_space_refine
on Tue Jan 13 23:35:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqx_26074/01_2026/7tqx_26074.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
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: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      2      5.21       5
     S      63      5.16       5
     C    6137      2.51       5
     N    1703      2.21       5
     O    1909      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9822
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3437
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3376
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 20, 'TRANS': 408}
    Chain: "K"
      Number of atoms: 2854
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 360, 2839
          Classifications: {'peptide': 360}
          Link IDs: {'PTRANS': 14, 'TRANS': 345}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 360, 2839
          Classifications: {'peptide': 360}
          Link IDs: {'PTRANS': 14, 'TRANS': 345}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2860
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.85, per 1000 atoms: 0.29
  Number of scatterers: 9822
  At special positions: 0
  Unit cell: (109.725, 72.6, 109.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P       8     15.00
     Mg      2     11.99
     O    1909      8.00
     N    1703      7.00
     C    6137      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.92
  Conformation dependent library (CDL) restraints added in 566.9 milliseconds
  

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2296

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 7 sheets defined
      49.6% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 42
      removed outlier: 4.522A  pdb=" N   LYS A  40 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 82 through 85
      removed outlier: 4.618A  pdb=" N   GLN A  85 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 85'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 128
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.189A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
    Processing helix  chain 'A' and resid 190 through 197
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.625A  pdb=" N   ILE A 209 " --> pdb=" O   ASP A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 3.648A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.219A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.840A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.002A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.792A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 4.353A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG A 422 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLY A 436 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 3.926A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 79
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.533A  pdb=" N   PHE B  85 " --> pdb=" O   GLY B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 107 through 126
      removed outlier: 4.063A  pdb=" N   GLU B 111 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
    Processing helix  chain 'B' and resid 180 through 193
      removed outlier: 3.675A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.501A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 275 through 282
      removed outlier: 4.273A  pdb=" N   GLN B 279 " --> pdb=" O   ARG B 276 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   GLN B 280 " --> pdb=" O   GLY B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 294
    Processing helix  chain 'B' and resid 295 through 299
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.731A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA B 387 " --> pdb=" O   GLU B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 404 through 425
      removed outlier: 3.841A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 44
      removed outlier: 3.560A  pdb=" N   ASN K  41 " --> pdb=" O   GLU K  37 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG K  42 " --> pdb=" O   ALA K  38 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 124 through 132
      removed outlier: 4.549A  pdb=" N   ASN K 130 " --> pdb=" O   LYS K 126 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 157 through 166
      removed outlier: 3.804A  pdb=" N   VAL K 161 " --> pdb=" O   THR K 157 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 166 through 176
      removed outlier: 3.642A  pdb=" N   LEU K 170 " --> pdb=" O   THR K 166 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ASP K 171 " --> pdb=" O   GLN K 167 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER K 172 " --> pdb=" O   PRO K 168 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 190 through 196
    Processing helix  chain 'K' and resid 203 through 219
    Processing helix  chain 'K' and resid 274 through 288
    Processing helix  chain 'K' and resid 347 through 372
      removed outlier: 3.875A  pdb=" N   ASN K 351 " --> pdb=" O   GLY K 347 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 373 through 378
      removed outlier: 3.862A  pdb=" N   ARG K 376 " --> pdb=" O   PRO K 373 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ASN K 377 " --> pdb=" O   ARG K 374 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS K 378 " --> pdb=" O   ARG K 375 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 373 through 378'
    Processing helix  chain 'K' and resid 380 through 383
      removed outlier: 3.556A  pdb=" N   ASP K 383 " --> pdb=" O   PRO K 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 380 through 383'
    Processing helix  chain 'K' and resid 384 through 390
    Processing helix  chain 'K' and resid 409 through 411
      No H-bonds generated for 'chain 'K' and resid 409 through 411'
    Processing helix  chain 'K' and resid 412 through 425
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
      removed outlier: 8.486A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272
    Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92
      removed outlier: 7.992A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 7.158A  pdb=" N   GLN B 131 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   ASN B 165 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE B 133 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   PHE B 167 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   VAL B 169 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   HIS B 137 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ASP B 203 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 11.845A  pdb=" N   PHE B 270 " --> pdb=" O   ASP B 203 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54
    Processing sheet with id=AA6, first strand: chain 'K' and resid 150 through 152
      removed outlier: 6.455A  pdb=" N   THR K 180 " --> pdb=" O   VAL K 401 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ILE K 403 " --> pdb=" O   THR K 180 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   PHE K 182 " --> pdb=" O   ILE K 403 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   CYS K 405 " --> pdb=" O   PHE K 182 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   TYR K 184 " --> pdb=" O   CYS K 405 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ALA K 179 " --> pdb=" O   SER K 330 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   ILE K 332 " --> pdb=" O   ALA K 179 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   VAL K 181 " --> pdb=" O   ILE K 332 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 106 through 110
      removed outlier: 6.635A  pdb=" N   MET K 113 " --> pdb=" O   VAL K 109 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1320 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: 1.59

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1789
        1.32 -     1.45: 2556
        1.45 -     1.57: 5565
        1.57 -     1.70: 19
        1.70 -     1.82: 98
  Bond restraints: 10027
  Sorted by residual:
  bond pdb=" O3A ANP K 502 "
       pdb=" PB  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.700  1.557  0.143 2.00e-02 2.50e+03 5.10e+01
  bond pdb=" N3B ANP K 502 "
       pdb=" PG  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.795  1.693  0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" O5' ANP K 502 "
       pdb=" PA  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.655  1.583  0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" N   ASP A 205 "
       pdb=" CA  ASP A 205 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.19e-02 7.06e+03 8.01e+00
  bond pdb=" N   CYS K 398 "
       pdb=" CA  CYS K 398 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.27e-02 6.20e+03 7.32e+00
  ... (remaining 10022 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.52: 13486
        3.52 -     7.04: 120
        7.04 -    10.56: 9
       10.56 -    14.09: 2
       14.09 -    17.61: 1
  Bond angle restraints: 13618
  Sorted by residual:
  angle pdb=" PB  ANP K 502 "
        pdb=" N3B ANP K 502 "
        pdb=" PG  ANP K 502 "
      ideal   model   delta    sigma   weight residual
     126.95  109.34   17.61 3.00e+00 1.11e-01 3.44e+01
  angle pdb=" CB  MET B 170 "
        pdb=" CG  MET B 170 "
        pdb=" SD  MET B 170 "
      ideal   model   delta    sigma   weight residual
     112.70  125.50  -12.80 3.00e+00 1.11e-01 1.82e+01
  angle pdb=" CB  LYS K 430 "
        pdb=" CG  LYS K 430 "
        pdb=" CD  LYS K 430 "
      ideal   model   delta    sigma   weight residual
     111.30  120.96   -9.66 2.30e+00 1.89e-01 1.76e+01
  angle pdb=" O1B ANP K 502 "
        pdb=" PB  ANP K 502 "
        pdb=" O2B ANP K 502 "
      ideal   model   delta    sigma   weight residual
     120.08  109.15   10.93 3.00e+00 1.11e-01 1.33e+01
  angle pdb=" CA  THR K 343 "
        pdb=" C   THR K 343 "
        pdb=" O   THR K 343 "
      ideal   model   delta    sigma   weight residual
     122.36  118.16    4.20 1.21e+00 6.83e-01 1.20e+01
  ... (remaining 13613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.56: 5880
       32.56 -    65.12: 203
       65.12 -    97.68: 35
       97.68 -   130.25: 4
      130.25 -   162.81: 9
  Dihedral angle restraints: 6131
    sinusoidal: 2563
      harmonic: 3568
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -127.92 -162.81     1      2.00e+01 2.50e-03 4.69e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -30.43  135.02     1      2.00e+01 2.50e-03 4.10e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12  160.30  113.82     1      2.00e+01 2.50e-03 3.37e+01
  ... (remaining 6128 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1203
       0.052 -    0.104: 230
       0.104 -    0.155: 75
       0.155 -    0.207: 2
       0.207 -    0.259: 1
  Chirality restraints: 1511
  Sorted by residual:
  chirality pdb=" C3' ANP K 502 "
            pdb=" C2' ANP K 502 "
            pdb=" C4' ANP K 502 "
            pdb=" O3' ANP K 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.62    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  ARG B 359 "
            pdb=" N   ARG B 359 "
            pdb=" C   ARG B 359 "
            pdb=" CB  ARG B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.49e-01
  chirality pdb=" CA  LEU K 350 "
            pdb=" N   LEU K 350 "
            pdb=" C   LEU K 350 "
            pdb=" CB  LEU K 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.82e-01
  ... (remaining 1508 not shown)

  Planarity restraints: 1768
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 390 "   -0.208 9.50e-02 1.11e+02   9.37e-02 5.95e+00
        pdb=" NE  ARG B 390 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 390 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 390 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 390 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE K 132 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.90e+00
        pdb=" N   PRO K 133 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO K 133 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO K 133 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA K 298 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.91e+00
        pdb=" C   ALA K 298 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ALA K 298 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   THR K 299 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1765 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 76
        2.56 -     3.15: 7762
        3.15 -     3.73: 14947
        3.73 -     4.32: 21134
        4.32 -     4.90: 36673
  Nonbonded interactions: 80592
  Sorted by model distance:
  nonbonded pdb=" O1G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.977 2.170
  nonbonded pdb=" O2B GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.985 2.170
  nonbonded pdb="MG    MG K 501 "
            pdb=" O1G ANP K 502 "
     model   vdw
     2.036 2.170
  nonbonded pdb=" OE2 GLU A  71 "
            pdb="MG    MG A 502 "
     model   vdw
     2.042 2.170
  nonbonded pdb="MG    MG K 501 "
            pdb=" O1B ANP K 502 "
     model   vdw
     2.100 2.170
  ... (remaining 80587 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=0.35 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:             4.790
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.320
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.143  10027  Z= 0.248
  Angle     :  0.820  17.607  13618  Z= 0.413
  Chirality :  0.046   0.259   1511
  Planarity :  0.005   0.094   1768
  Dihedral  : 18.243 162.807   3835
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 14.54 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.25), residues: 1223
  helix:  1.19 (0.24), residues: 499
  sheet: -0.34 (0.37), residues: 212
  loop : -0.92 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 390 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.010   0.001   PHE A  52 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.007   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 (10027)
  covalent geometry    : angle       0.82001 (13618)
  hydrogen bonds       : bond        0.15997 (  465)
  hydrogen bonds       : angle       6.12326 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 179
  time to evaluate  : 0.386 
Fit side-chains
REVERT: K  225 ILE cc_start: 0.8939 (mt) cc_final: 0.8702 (mm)
  outliers start: 5
  outliers final: 3
  residues processed: 179
  average time/residue: 0.5938
  time to fit residues: 113.6743
Evaluate side-chains
  173 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain K residue  259 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0570
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
A 256 GLN
B  99 ASN
B 100 ASN
B 134 GLN
B 204 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.119120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.094393 restraints weight = 28353.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 3.08
r_work: 0.3128 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10027  Z= 0.120
  Angle     :  0.563  10.228  13618  Z= 0.274
  Chirality :  0.044   0.354   1511
  Planarity :  0.004   0.057   1768
  Dihedral  : 11.544 155.826   1515
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.04 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.25), residues: 1223
  helix:  1.59 (0.24), residues: 519
  sheet:  0.01 (0.37), residues: 214
  loop : -0.83 (0.28), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 320 
 TYR   0.012   0.001   TYR A 103 
 PHE   0.008   0.001   PHE B 367 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.005   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10027)
  covalent geometry    : angle       0.56258 (13618)
  hydrogen bonds       : bond        0.04092 (  465)
  hydrogen bonds       : angle       4.45833 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 188
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8230 (mt-10)
REVERT: A  297 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7601 (mm-30)
REVERT: A  301 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8036 (mp-120)
REVERT: B   57 ASN cc_start: 0.7566 (t0) cc_final: 0.7344 (t0)
REVERT: B  209 ASP cc_start: 0.8253 (t0) cc_final: 0.7721 (t0)
REVERT: B  322 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8414 (t)
REVERT: B  390 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8496 (mtm-85)
REVERT: B  423 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8610 (tm-30)
REVERT: K  172 SER cc_start: 0.8672 (m) cc_final: 0.8445 (p)
REVERT: K  225 ILE cc_start: 0.9040 (mt) cc_final: 0.8796 (mp)
REVERT: K  430 LYS cc_start: 0.8329 (mmmm) cc_final: 0.8074 (mtmm)
  outliers start: 21
  outliers final: 5
  residues processed: 196
  average time/residue: 0.5546
  time to fit residues: 117.1916
Evaluate side-chains
  178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 171
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  208 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 64 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 119 optimal weight:    0.5980
   chunk 121 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 128 GLN
A 197 HIS
B  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.119467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.094191 restraints weight = 30875.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 3.26
r_work: 0.3123 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10027  Z= 0.108
  Angle     :  0.512   8.185  13618  Z= 0.253
  Chirality :  0.044   0.334   1511
  Planarity :  0.003   0.050   1768
  Dihedral  :  9.122 149.679   1508
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.95 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.73 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1223
  helix:  1.77 (0.24), residues: 520
  sheet:  0.28 (0.37), residues: 209
  loop : -0.81 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 320 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.009   0.001   PHE K 152 
 TRP   0.010   0.001   TRP A 388 
 HIS   0.004   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (10027)
  covalent geometry    : angle       0.51159 (13618)
  hydrogen bonds       : bond        0.03746 (  465)
  hydrogen bonds       : angle       4.22974 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8161 (m-30) cc_final: 0.7892 (m-30)
REVERT: B   26 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8509 (t0)
REVERT: B   57 ASN cc_start: 0.7624 (t0) cc_final: 0.7368 (t0)
REVERT: B  209 ASP cc_start: 0.8252 (t0) cc_final: 0.7747 (t0)
REVERT: B  322 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8376 (t)
REVERT: B  390 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8444 (mtm-85)
REVERT: B  423 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: K  172 SER cc_start: 0.8726 (m) cc_final: 0.8476 (t)
REVERT: K  225 ILE cc_start: 0.9030 (mt) cc_final: 0.8770 (mp)
REVERT: K  333 ASP cc_start: 0.7729 (t0) cc_final: 0.7486 (t0)
REVERT: K  430 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8126 (mtmp)
  outliers start: 25
  outliers final: 10
  residues processed: 196
  average time/residue: 0.5374
  time to fit residues: 113.7433
Evaluate side-chains
  191 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 179
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  303 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 108 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  18 ASN
A  31 GLN
A  61 HIS
B 264 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.118455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.093823 restraints weight = 25916.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.93
r_work: 0.3127 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10027  Z= 0.120
  Angle     :  0.511   9.522  13618  Z= 0.253
  Chirality :  0.043   0.265   1511
  Planarity :  0.003   0.054   1768
  Dihedral  :  8.976 145.439   1508
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.95 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.04 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1223
  helix:  1.82 (0.24), residues: 518
  sheet:  0.33 (0.37), residues: 209
  loop : -0.75 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 339 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.009   0.001   PHE A 149 
 TRP   0.010   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10027)
  covalent geometry    : angle       0.51100 (13618)
  hydrogen bonds       : bond        0.03678 (  465)
  hydrogen bonds       : angle       4.16935 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8167 (m-30) cc_final: 0.7892 (m-30)
REVERT: B   57 ASN cc_start: 0.7671 (t0) cc_final: 0.7395 (t0)
REVERT: B  209 ASP cc_start: 0.8229 (t0) cc_final: 0.7722 (t0)
REVERT: B  299 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8643 (mmt)
REVERT: B  322 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8379 (t)
REVERT: B  423 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: K  172 SER cc_start: 0.8717 (m) cc_final: 0.8493 (t)
  outliers start: 24
  outliers final: 14
  residues processed: 195
  average time/residue: 0.5632
  time to fit residues: 118.2192
Evaluate side-chains
  198 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  386 GLU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  105 ILE
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  303 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 105 optimal weight:    0.0370
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.7862

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.118570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.093135 restraints weight = 31037.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.26
r_work: 0.3106 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10027  Z= 0.118
  Angle     :  0.517   9.748  13618  Z= 0.255
  Chirality :  0.043   0.222   1511
  Planarity :  0.003   0.051   1768
  Dihedral  :  8.803 140.315   1508
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.03 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.42 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.25), residues: 1223
  helix:  1.87 (0.23), residues: 518
  sheet:  0.38 (0.37), residues: 210
  loop : -0.75 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 339 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.009   0.001   PHE A 149 
 TRP   0.010   0.001   TRP A  21 
 HIS   0.005   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10027)
  covalent geometry    : angle       0.51731 (13618)
  hydrogen bonds       : bond        0.03619 (  465)
  hydrogen bonds       : angle       4.12260 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8145 (m-30) cc_final: 0.7880 (m-30)
REVERT: B   26 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8518 (t0)
REVERT: B   57 ASN cc_start: 0.7737 (t0) cc_final: 0.7454 (t0)
REVERT: B  209 ASP cc_start: 0.8296 (t0) cc_final: 0.7778 (t0)
REVERT: B  322 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8397 (t)
REVERT: B  388 MET cc_start: 0.8791 (mtp) cc_final: 0.8554 (mtm)
REVERT: B  423 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8532 (tm-30)
REVERT: K  172 SER cc_start: 0.8704 (m) cc_final: 0.8490 (t)
REVERT: K  424 ASP cc_start: 0.8784 (t70) cc_final: 0.8468 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 194
  average time/residue: 0.5503
  time to fit residues: 114.9230
Evaluate side-chains
  196 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  105 ILE
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  264 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 108 optimal weight:    9.9990
   chunk 119 optimal weight:    8.9990
   chunk 103 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 107 HIS
B  99 ASN
K 158 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.115802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.091379 restraints weight = 21986.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.70
r_work: 0.3098 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3099 r_free = 0.3099    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10027  Z= 0.198
  Angle     :  0.560   9.900  13618  Z= 0.279
  Chirality :  0.045   0.212   1511
  Planarity :  0.004   0.052   1768
  Dihedral  :  8.920 141.176   1508
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.42 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1223
  helix:  1.83 (0.23), residues: 517
  sheet:  0.30 (0.37), residues: 220
  loop : -0.85 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 339 
 TYR   0.008   0.001   TYR K 235 
 PHE   0.013   0.001   PHE B 408 
 TRP   0.011   0.002   TRP B  21 
 HIS   0.007   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 (10027)
  covalent geometry    : angle       0.55965 (13618)
  hydrogen bonds       : bond        0.04249 (  465)
  hydrogen bonds       : angle       4.27729 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  168 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7589 (tt0)
REVERT: A  211 ASP cc_start: 0.8123 (m-30) cc_final: 0.7853 (m-30)
REVERT: A  417 GLU cc_start: 0.8009 (tt0) cc_final: 0.7697 (mt-10)
REVERT: B   26 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8555 (t0)
REVERT: B   57 ASN cc_start: 0.7798 (t0) cc_final: 0.7470 (t0)
REVERT: B  209 ASP cc_start: 0.8308 (t0) cc_final: 0.7762 (t0)
REVERT: B  322 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8406 (t)
REVERT: B  388 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8519 (mtm)
REVERT: B  423 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8489 (tm-30)
REVERT: K  415 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8145 (mt-10)
REVERT: K  424 ASP cc_start: 0.8790 (t70) cc_final: 0.8471 (t0)
  outliers start: 28
  outliers final: 16
  residues processed: 203
  average time/residue: 0.5735
  time to fit residues: 124.8816
Evaluate side-chains
  203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 183
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  388 MET
Chi-restraints excluded: chain K residue  105 ILE
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  264 VAL
Chi-restraints excluded: chain K residue  303 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 112 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.116683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.090448 restraints weight = 38853.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 3.65
r_work: 0.3041 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3041
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3041 r_free = 0.3041    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3041
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10027  Z= 0.158
  Angle     :  0.546  10.535  13618  Z= 0.273
  Chirality :  0.045   0.319   1511
  Planarity :  0.004   0.050   1768
  Dihedral  :  8.796 140.547   1508
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.19 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.45 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1223
  helix:  1.88 (0.23), residues: 512
  sheet:  0.32 (0.37), residues: 210
  loop : -0.88 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 320 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.010   0.001   PHE B 408 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.005   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10027)
  covalent geometry    : angle       0.54561 (13618)
  hydrogen bonds       : bond        0.03949 (  465)
  hydrogen bonds       : angle       4.24064 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8205 (m-30) cc_final: 0.7962 (m-30)
REVERT: A  417 GLU cc_start: 0.8120 (tt0) cc_final: 0.7826 (mt-10)
REVERT: B   26 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8597 (t0)
REVERT: B   57 ASN cc_start: 0.7910 (t0) cc_final: 0.7521 (t0)
REVERT: B  209 ASP cc_start: 0.8443 (t0) cc_final: 0.7878 (t0)
REVERT: B  322 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8440 (t)
REVERT: B  388 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8600 (mtm)
REVERT: B  423 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8596 (tm-30)
REVERT: K  415 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8295 (mt-10)
REVERT: K  424 ASP cc_start: 0.8854 (t70) cc_final: 0.8542 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 202
  average time/residue: 0.5472
  time to fit residues: 119.2428
Evaluate side-chains
  209 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  388 MET
Chi-restraints excluded: chain K residue  105 ILE
Chi-restraints excluded: chain K residue  127 MET
Chi-restraints excluded: chain K residue  153 ASP
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  264 VAL
Chi-restraints excluded: chain K residue  303 SER
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 119 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0010
   chunk 70 optimal weight:    0.6980
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.116962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.092431 restraints weight = 22639.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.76
r_work: 0.3110 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10027  Z= 0.144
  Angle     :  0.554  11.809  13618  Z= 0.273
  Chirality :  0.044   0.290   1511
  Planarity :  0.004   0.051   1768
  Dihedral  :  8.704 139.207   1508
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.87 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.20 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.25), residues: 1223
  helix:  1.90 (0.24), residues: 511
  sheet:  0.31 (0.37), residues: 210
  loop : -0.91 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 339 
 TYR   0.009   0.001   TYR A 103 
 PHE   0.010   0.001   PHE A 149 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.005   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (10027)
  covalent geometry    : angle       0.55403 (13618)
  hydrogen bonds       : bond        0.03875 (  465)
  hydrogen bonds       : angle       4.21569 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8106 (m-30) cc_final: 0.7857 (m-30)
REVERT: A  417 GLU cc_start: 0.7969 (tt0) cc_final: 0.7691 (mt-10)
REVERT: B   26 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8513 (t0)
REVERT: B   57 ASN cc_start: 0.7862 (t0) cc_final: 0.7465 (t0)
REVERT: B  203 ASP cc_start: 0.7788 (m-30) cc_final: 0.7522 (m-30)
REVERT: B  209 ASP cc_start: 0.8331 (t0) cc_final: 0.7775 (t0)
REVERT: B  322 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8377 (t)
REVERT: B  388 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (mtm)
REVERT: B  423 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8516 (tm-30)
REVERT: K  415 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8218 (mt-10)
REVERT: K  424 ASP cc_start: 0.8794 (t70) cc_final: 0.8484 (t0)
  outliers start: 28
  outliers final: 21
  residues processed: 196
  average time/residue: 0.5473
  time to fit residues: 115.4121
Evaluate side-chains
  207 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   26 ASP
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  388 MET
Chi-restraints excluded: chain K residue  105 ILE
Chi-restraints excluded: chain K residue  127 MET
Chi-restraints excluded: chain K residue  153 ASP
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  230 SER
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  264 VAL
Chi-restraints excluded: chain K residue  303 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 72 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0050
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.118688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.093097 restraints weight = 30918.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 3.26
r_work: 0.3101 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10027  Z= 0.112
  Angle     :  0.531  12.172  13618  Z= 0.263
  Chirality :  0.043   0.276   1511
  Planarity :  0.004   0.051   1768
  Dihedral  :  8.469 134.784   1508
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.67 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1223
  helix:  1.98 (0.24), residues: 512
  sheet:  0.34 (0.36), residues: 210
  loop : -0.88 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 339 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.009   0.001   PHE A 149 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.003   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10027)
  covalent geometry    : angle       0.53082 (13618)
  hydrogen bonds       : bond        0.03516 (  465)
  hydrogen bonds       : angle       4.13379 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8156 (m-30) cc_final: 0.7908 (m-30)
REVERT: A  417 GLU cc_start: 0.8041 (tt0) cc_final: 0.7768 (mt-10)
REVERT: B   57 ASN cc_start: 0.7869 (t0) cc_final: 0.7484 (t0)
REVERT: B  203 ASP cc_start: 0.7819 (m-30) cc_final: 0.7590 (m-30)
REVERT: B  209 ASP cc_start: 0.8400 (t0) cc_final: 0.7860 (t0)
REVERT: B  322 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8382 (t)
REVERT: B  388 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8580 (mtm)
REVERT: B  423 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8526 (tm-30)
REVERT: K  312 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8442 (pt)
REVERT: K  415 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: K  424 ASP cc_start: 0.8828 (t70) cc_final: 0.8519 (t0)
  outliers start: 24
  outliers final: 13
  residues processed: 198
  average time/residue: 0.5363
  time to fit residues: 115.0740
Evaluate side-chains
  203 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 187
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   99 ASN
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  388 MET
Chi-restraints excluded: chain K residue  109 VAL
Chi-restraints excluded: chain K residue  127 MET
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  264 VAL
Chi-restraints excluded: chain K residue  303 SER
Chi-restraints excluded: chain K residue  312 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 309 HIS
B  99 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.118367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.093007 restraints weight = 29998.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 3.18
r_work: 0.3101 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10027  Z= 0.127
  Angle     :  0.535  12.326  13618  Z= 0.265
  Chirality :  0.044   0.267   1511
  Planarity :  0.004   0.051   1768
  Dihedral  :  8.414 133.224   1508
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.95 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.04 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.25), residues: 1223
  helix:  2.00 (0.24), residues: 511
  sheet:  0.39 (0.37), residues: 210
  loop : -0.87 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 339 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.009   0.001   PHE A 149 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10027)
  covalent geometry    : angle       0.53512 (13618)
  hydrogen bonds       : bond        0.03614 (  465)
  hydrogen bonds       : angle       4.12339 ( 1320)

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  211 ASP cc_start: 0.8134 (m-30) cc_final: 0.7881 (m-30)
REVERT: A  417 GLU cc_start: 0.7978 (tt0) cc_final: 0.7752 (mt-10)
REVERT: B   57 ASN cc_start: 0.7839 (t0) cc_final: 0.7455 (t0)
REVERT: B  203 ASP cc_start: 0.7826 (m-30) cc_final: 0.7548 (m-30)
REVERT: B  209 ASP cc_start: 0.8393 (t0) cc_final: 0.7842 (t0)
REVERT: B  322 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8386 (t)
REVERT: B  423 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8500 (tm-30)
REVERT: K  312 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8445 (pt)
REVERT: K  415 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8316 (mt-10)
REVERT: K  424 ASP cc_start: 0.8821 (t70) cc_final: 0.8518 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 198
  average time/residue: 0.5354
  time to fit residues: 114.4478
Evaluate side-chains
  205 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 188
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue  130 THR
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  109 VAL
Chi-restraints excluded: chain K residue  127 MET
Chi-restraints excluded: chain K residue  153 ASP
Chi-restraints excluded: chain K residue  225 ILE
Chi-restraints excluded: chain K residue  264 VAL
Chi-restraints excluded: chain K residue  303 SER
Chi-restraints excluded: chain K residue  312 ILE
Chi-restraints excluded: chain K residue  315 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 117 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0370
   chunk 95 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 309 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.118718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.094208 restraints weight = 22545.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.74
r_work: 0.3142 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10027  Z= 0.119
  Angle     :  0.540  12.341  13618  Z= 0.265
  Chirality :  0.043   0.260   1511
  Planarity :  0.004   0.051   1768
  Dihedral  :  8.380 132.067   1508
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.23 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.25), residues: 1223
  helix:  2.01 (0.24), residues: 511
  sheet:  0.43 (0.37), residues: 210
  loop : -0.86 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 339 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.010   0.001   PHE B 408 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.004   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10027)
  covalent geometry    : angle       0.54017 (13618)
  hydrogen bonds       : bond        0.03569 (  465)
  hydrogen bonds       : angle       4.11915 ( 1320)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3730.53 seconds
wall clock time: 64 minutes 24.23 seconds (3864.23 seconds total)