Starting phenix.real_space_refine
on Tue Jan 13 23:45:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqy_26075/01_2026/7tqy_26075.map"
  }
  resolution = 2.6
  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=   0.005
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       7      5.49       5
     Mg      2      5.21       5
     S      63      5.16       5
     C    6182      2.51       5
     N    1712      2.21       5
     O    1920      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 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: 9890
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "K"
      Number of atoms: 2913
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 365, 2893
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 14, 'TRANS': 350}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 365, 2893
          Classifications: {'peptide': 365}
          Link IDs: {'PTRANS': 14, 'TRANS': 350}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2909
    Chain: "A"
      Number of atoms: 3446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3446
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 20, 'TRANS': 420}
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3376
          Classifications: {'peptide': 429}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408}
    Chain: "K"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    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}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR K 422 " occ=0.40
      ... (22 atoms not shown)
      pdb=" OH BTYR K 422 " occ=0.60
  Time building chain proxies: 2.89, per 1000 atoms: 0.29
  Number of scatterers: 9890
  At special positions: 0
  Unit cell: (109.521, 68.769, 110.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      63     16.00
     P       7     15.00
     Al      1     13.00
     Mg      2     11.99
     F       3      9.00
     O    1920      8.00
     N    1712      7.00
     C    6182      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: 0.89
  Conformation dependent library (CDL) restraints added in 691.3 milliseconds
  

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2312

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 10 sheets defined
      49.6% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'K' and resid 36 through 48
    Processing helix  chain 'K' and resid 122 through 130
    Processing helix  chain 'K' and resid 157 through 166
    Processing helix  chain 'K' and resid 166 through 176
    Processing helix  chain 'K' and resid 190 through 196
    Processing helix  chain 'K' and resid 203 through 219
    Processing helix  chain 'K' and resid 248 through 252
    Processing helix  chain 'K' and resid 274 through 288
      removed outlier: 3.583A  pdb=" N   ASN K 288 " --> pdb=" O   GLU K 284 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 347 through 372
    Processing helix  chain 'K' and resid 373 through 376
    Processing helix  chain 'K' and resid 380 through 383
      removed outlier: 3.834A  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 390 through 396
      removed outlier: 3.564A  pdb=" N   LEU K 394 " --> pdb=" O   LEU K 390 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLY K 396 " --> pdb=" O   PHE K 392 " (cutoff:3.500A)
    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 427
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 41
    Processing helix  chain 'A' and resid 71 through 80
      removed outlier: 4.586A  pdb=" N   ILE A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 114 through 128
      removed outlier: 3.680A  pdb=" N   GLN A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 4.118A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 240
      removed outlier: 3.765A  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
      removed outlier: 4.066A  pdb=" N   PHE A 255 " --> pdb=" O   ASP A 251 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.838A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.707A  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 337
      removed outlier: 3.518A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 3.900A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 4.228A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 40 through 44
      removed outlier: 3.550A  pdb=" N   GLN B  43 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU B  44 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 40 through 44'
    Processing helix  chain 'B' and resid 46 through 49
    Processing helix  chain 'B' and resid 69 through 79
      removed outlier: 4.464A  pdb=" N   MET B  73 " --> pdb=" O   GLU B  69 " (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 108 through 125
      removed outlier: 3.665A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 159
    Processing helix  chain 'B' and resid 180 through 194
      removed outlier: 3.544A  pdb=" N   ASN B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 214
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.830A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 242
      removed outlier: 3.890A  pdb=" N   ARG B 241 " --> pdb=" O   THR B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 258
    Processing helix  chain 'B' and resid 277 through 282
      removed outlier: 3.966A  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
      removed outlier: 3.603A  pdb=" N   MET B 299 " --> pdb=" O   SER B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
      removed outlier: 3.662A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLN B 334 " --> pdb=" O   MET B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 374 through 390
      removed outlier: 3.545A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 3.904A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'K' and resid 150 through 152
      removed outlier: 3.752A  pdb=" N   ARG K 150 " --> pdb=" O   VAL K  28 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   SER K  27 " --> pdb=" O   MET K 402 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   VAL K 404 " --> pdb=" O   SER K  27 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ALA K  29 " --> pdb=" O   VAL K 404 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   VAL K 406 " --> pdb=" O   ALA K  29 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ARG K  31 " --> pdb=" O   VAL K 406 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 106 through 110
      removed outlier: 6.555A  pdb=" N   MET K 113 " --> pdb=" O   VAL K 109 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 197 through 198
    Processing sheet with id=AA5, first strand: chain 'K' and resid 291 through 292
    Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.361A  pdb=" N   GLU A   3 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
      removed outlier: 8.558A  pdb=" N   LEU A 136 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   PHE A 138 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ILE A   7 " --> pdb=" O   PHE A 138 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   SER A 140 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 8.775A  pdb=" N   VAL A   9 " --> pdb=" O   SER A 140 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   GLN A 133 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   LEU A 167 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   PHE A 135 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 272
    Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 92
      removed outlier: 8.139A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   MET B 164 " --> pdb=" O   GLU B 198 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   TYR B 200 " --> pdb=" O   MET B 164 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   THR B 166 " --> pdb=" O   TYR B 200 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   ILE B 202 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   SER B 168 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.425A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 51 through 53

    479 hydrogen bonds defined for protein.
    1354 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: 1.43

  Time building geometry restraints manager: 1.16 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: 1763
        1.32 -     1.45: 2620
        1.45 -     1.57: 5596
        1.57 -     1.70: 19
        1.70 -     1.82: 98
  Bond restraints: 10096
  Sorted by residual:
  bond pdb=" C   PHE K 326 "
       pdb=" O   PHE K 326 "
    ideal  model  delta    sigma   weight residual
    1.234  1.301 -0.067 1.30e-02 5.92e+03 2.67e+01
  bond pdb=" N   ASP A  98 "
       pdb=" CA  ASP A  98 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.17e-02 7.31e+03 9.38e+00
  bond pdb=" N   PHE K 326 "
       pdb=" CA BPHE K 326 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.18e-02 7.18e+03 8.23e+00
  bond pdb=" N   PHE K 326 "
       pdb=" CA APHE K 326 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.18e-02 7.18e+03 8.03e+00
  bond pdb=" N   VAL A 344 "
       pdb=" CA  VAL A 344 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.19e-02 7.06e+03 7.87e+00
  ... (remaining 10091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 13255
        2.08 -     4.16: 365
        4.16 -     6.24: 82
        6.24 -     8.31: 6
        8.31 -    10.39: 2
  Bond angle restraints: 13710
  Sorted by residual:
  angle pdb=" N   THR A  94 "
        pdb=" CA  THR A  94 "
        pdb=" C   THR A  94 "
      ideal   model   delta    sigma   weight residual
     111.30  100.91   10.39 1.43e+00 4.89e-01 5.28e+01
  angle pdb=" N   LYS A  96 "
        pdb=" CA  LYS A  96 "
        pdb=" C   LYS A  96 "
      ideal   model   delta    sigma   weight residual
     112.38  105.91    6.47 1.22e+00 6.72e-01 2.82e+01
  angle pdb=" O   PHE K 326 "
        pdb=" C   PHE K 326 "
        pdb=" CA BPHE K 326 "
      ideal   model   delta    sigma   weight residual
     120.43  125.84   -5.41 1.18e+00 7.18e-01 2.11e+01
  angle pdb=" O   PHE K 326 "
        pdb=" C   PHE K 326 "
        pdb=" CA APHE K 326 "
      ideal   model   delta    sigma   weight residual
     120.43  125.49   -5.06 1.18e+00 7.18e-01 1.84e+01
  angle pdb=" N   ILE A 114 "
        pdb=" CA  ILE A 114 "
        pdb=" C   ILE A 114 "
      ideal   model   delta    sigma   weight residual
     113.71  109.72    3.99 9.50e-01 1.11e+00 1.77e+01
  ... (remaining 13705 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.50: 5864
       30.50 -    60.99: 236
       60.99 -    91.48: 38
       91.48 -   121.98: 1
      121.98 -   152.47: 12
  Dihedral angle restraints: 6151
    sinusoidal: 2560
      harmonic: 3591
  Sorted by residual:
  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  -47.88  152.47     1      2.00e+01 2.50e-03 4.53e+01
  dihedral pdb=" O1B ADP K 801 "
           pdb=" O3A ADP K 801 "
           pdb=" PB  ADP K 801 "
           pdb=" PA  ADP K 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  159.88  140.12     1      2.00e+01 2.50e-03 4.24e+01
  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 -176.02 -114.71     1      2.00e+01 2.50e-03 3.40e+01
  ... (remaining 6148 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 969
       0.039 -    0.077: 393
       0.077 -    0.116: 107
       0.116 -    0.155: 46
       0.155 -    0.193: 6
  Chirality restraints: 1521
  Sorted by residual:
  chirality pdb=" CA  VAL A 344 "
            pdb=" N   VAL A 344 "
            pdb=" C   VAL A 344 "
            pdb=" CB  VAL A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" C10 TA1 B 502 "
            pdb=" C02 TA1 B 502 "
            pdb=" C11 TA1 B 502 "
            pdb=" C18 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.36    0.18 2.00e-01 2.50e+01 7.94e-01
  chirality pdb=" CA  ILE A  93 "
            pdb=" N   ILE A  93 "
            pdb=" C   ILE A  93 "
            pdb=" CB  ILE A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 1518 not shown)

  Planarity restraints: 1781
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  93 "    0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   ILE A  93 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   ILE A  93 "    0.022 2.00e-02 2.50e+03
        pdb=" N   THR A  94 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS K 344 "    0.013 2.00e-02 2.50e+03   2.77e-02 7.69e+00
        pdb=" C   LYS K 344 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LYS K 344 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASN K 345 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 384 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.87e+00
        pdb=" C   GLN B 384 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   GLN B 384 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE B 385 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1778 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 32
        2.54 -     3.13: 7327
        3.13 -     3.72: 15108
        3.72 -     4.31: 21670
        4.31 -     4.90: 37100
  Nonbonded interactions: 81237
  Sorted by model distance:
  nonbonded pdb=" O3G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     1.947 2.170
  nonbonded pdb=" OG  SER K 301 "
            pdb="MG    MG K 802 "
     model   vdw
     2.012 2.170
  nonbonded pdb=" F3  AF3 K 800 "
            pdb="MG    MG K 802 "
     model   vdw
     2.071 2.120
  nonbonded pdb=" O   ASN A 186 "
            pdb=" OG1 THR A 190 "
     model   vdw
     2.110 3.040
  nonbonded pdb=" O2B ADP K 801 "
            pdb="MG    MG K 802 "
     model   vdw
     2.133 2.170
  ... (remaining 81232 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=0.40 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:             5.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  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:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
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   0.067  10096  Z= 0.240
  Angle     :  0.847  10.393  13710  Z= 0.456
  Chirality :  0.048   0.193   1521
  Planarity :  0.005   0.054   1781
  Dihedral  : 18.154 152.475   3839
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 17.23 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.37 (0.24), residues: 1231
  helix:  1.07 (0.23), residues: 497
  sheet:  0.70 (0.38), residues: 192
  loop : -0.66 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG K 346 
 TYR   0.035   0.002   TYR B  36 
 PHE   0.023   0.002   PHE K 182 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.009   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (10096)
  covalent geometry    : angle       0.84654 (13710)
  hydrogen bonds       : bond        0.16265 (  479)
  hydrogen bonds       : angle       6.17345 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 222
  time to evaluate  : 0.389 
Fit side-chains
REVERT: K  113 MET cc_start: 0.7382 (tpp) cc_final: 0.7179 (tpt)
REVERT: K  288 ASN cc_start: 0.7978 (m-40) cc_final: 0.7745 (m110)
REVERT: K  402 MET cc_start: 0.8492 (ttm) cc_final: 0.7901 (ttt)
REVERT: B   58 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (tttp)
REVERT: B  108 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7632 (mm-30)
REVERT: B  417 ASP cc_start: 0.7791 (t70) cc_final: 0.7501 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 232
  average time/residue: 0.5535
  time to fit residues: 137.8936
Evaluate side-chains
  222 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 214
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  172 SER
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  420 GLU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  429 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.0870
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 117 optimal weight:    2.9990
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:
K 412 HIS
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 ASN
B 165 ASN
B 204 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.134178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.107746 restraints weight = 31460.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.89
r_work: 0.3326 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10096  Z= 0.150
  Angle     :  0.603  10.206  13710  Z= 0.299
  Chirality :  0.046   0.405   1521
  Planarity :  0.004   0.043   1781
  Dihedral  : 10.952 151.050   1507
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 14.71 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.98 (0.24), residues: 1231
  helix:  1.85 (0.23), residues: 508
  sheet:  0.78 (0.36), residues: 215
  loop : -0.63 (0.28), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 262 
 TYR   0.015   0.002   TYR B 310 
 PHE   0.015   0.001   PHE K 182 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (10096)
  covalent geometry    : angle       0.60308 (13710)
  hydrogen bonds       : bond        0.04359 (  479)
  hydrogen bonds       : angle       4.51286 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 226
  time to evaluate  : 0.417 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9004 (mt) cc_final: 0.8553 (tp)
REVERT: K  312 ILE cc_start: 0.8158 (mt) cc_final: 0.7925 (mm)
REVERT: K  402 MET cc_start: 0.8444 (ttm) cc_final: 0.8111 (ttt)
REVERT: B  108 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7874 (mm-30)
REVERT: B  125 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7120 (mp0)
REVERT: B  372 THR cc_start: 0.8610 (p) cc_final: 0.8353 (m)
REVERT: B  424 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8112 (tp40)
  outliers start: 33
  outliers final: 17
  residues processed: 242
  average time/residue: 0.5300
  time to fit residues: 138.2433
Evaluate side-chains
  223 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   25 SER
Chi-restraints excluded: chain K residue  153 ASP
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  174 LEU
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 107 HIS
A 133 GLN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 ASN
B 291 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.132430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.106879 restraints weight = 25982.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.58
r_work: 0.3333 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10096  Z= 0.178
  Angle     :  0.596   7.621  13710  Z= 0.298
  Chirality :  0.046   0.332   1521
  Planarity :  0.004   0.047   1781
  Dihedral  :  9.313 151.160   1495
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.48 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.24), residues: 1231
  helix:  1.91 (0.23), residues: 509
  sheet:  0.68 (0.35), residues: 221
  loop : -0.59 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 103 
 TYR   0.012   0.002   TYR B 310 
 PHE   0.017   0.002   PHE A 395 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (10096)
  covalent geometry    : angle       0.59632 (13710)
  hydrogen bonds       : bond        0.04589 (  479)
  hydrogen bonds       : angle       4.42789 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 215
  time to evaluate  : 0.374 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9029 (mt) cc_final: 0.8564 (tp)
REVERT: K  312 ILE cc_start: 0.8235 (mt) cc_final: 0.8010 (mm)
REVERT: K  402 MET cc_start: 0.8572 (ttm) cc_final: 0.8264 (ttt)
REVERT: A   36 MET cc_start: 0.8035 (ttt) cc_final: 0.7793 (ttt)
REVERT: A  431 ASP cc_start: 0.8098 (m-30) cc_final: 0.7865 (m-30)
REVERT: B  125 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7413 (mp0)
REVERT: B  372 THR cc_start: 0.8768 (p) cc_final: 0.8461 (m)
REVERT: B  424 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8279 (tp40)
  outliers start: 31
  outliers final: 17
  residues processed: 229
  average time/residue: 0.5775
  time to fit residues: 141.7021
Evaluate side-chains
  226 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 207
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 133 GLN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 ASN
B 291 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.132807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.107796 restraints weight = 23969.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.48
r_work: 0.3349 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10096  Z= 0.157
  Angle     :  0.568   6.630  13710  Z= 0.284
  Chirality :  0.045   0.257   1521
  Planarity :  0.004   0.046   1781
  Dihedral  :  9.200 150.405   1495
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.48 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.24), residues: 1231
  helix:  1.95 (0.23), residues: 515
  sheet:  0.81 (0.35), residues: 221
  loop : -0.66 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 103 
 TYR   0.014   0.001   TYR B 310 
 PHE   0.015   0.002   PHE K 182 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10096)
  covalent geometry    : angle       0.56780 (13710)
  hydrogen bonds       : bond        0.04218 (  479)
  hydrogen bonds       : angle       4.34560 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 212
  time to evaluate  : 0.438 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9000 (mt) cc_final: 0.8592 (tp)
REVERT: K  228 SER cc_start: 0.8504 (t) cc_final: 0.8219 (m)
REVERT: K  239 ILE cc_start: 0.8743 (mm) cc_final: 0.8542 (mt)
REVERT: K  312 ILE cc_start: 0.8191 (mt) cc_final: 0.7975 (mm)
REVERT: K  402 MET cc_start: 0.8529 (ttm) cc_final: 0.8237 (ttt)
REVERT: A  411 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7540 (mm-30)
REVERT: A  431 ASP cc_start: 0.8081 (m-30) cc_final: 0.7844 (m-30)
REVERT: B  162 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7432 (mmp-170)
REVERT: B  372 THR cc_start: 0.8759 (p) cc_final: 0.8435 (m)
REVERT: B  424 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (tp40)
  outliers start: 38
  outliers final: 19
  residues processed: 229
  average time/residue: 0.5713
  time to fit residues: 140.1198
Evaluate side-chains
  229 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  406 MET
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 41 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
K 164 ASN
K 345 ASN
** A  61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 133 GLN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 ASN
B 291 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.130421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.106258 restraints weight = 19451.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 2.17
r_work: 0.3334 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  10096  Z= 0.286
  Angle     :  0.652   9.588  13710  Z= 0.327
  Chirality :  0.049   0.218   1521
  Planarity :  0.005   0.050   1781
  Dihedral  :  9.387 150.034   1495
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 16.85 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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 (0.24), residues: 1231
  helix:  1.75 (0.23), residues: 505
  sheet:  1.01 (0.35), residues: 214
  loop : -0.80 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K 103 
 TYR   0.012   0.002   TYR B 183 
 PHE   0.020   0.002   PHE A 395 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.007   0.002   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00714 (10096)
  covalent geometry    : angle       0.65230 (13710)
  hydrogen bonds       : bond        0.05212 (  479)
  hydrogen bonds       : angle       4.52935 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 224
  time to evaluate  : 0.357 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9003 (mt) cc_final: 0.8615 (tp)
REVERT: K  153 ASP cc_start: 0.7895 (t70) cc_final: 0.7676 (m-30)
REVERT: K  209 MET cc_start: 0.8265 (mmp) cc_final: 0.8042 (mmp)
REVERT: K  228 SER cc_start: 0.8515 (t) cc_final: 0.8207 (m)
REVERT: K  312 ILE cc_start: 0.8224 (mt) cc_final: 0.8007 (mm)
REVERT: K  402 MET cc_start: 0.8550 (ttm) cc_final: 0.8263 (ttt)
REVERT: A  252 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8725 (mp)
REVERT: A  265 ILE cc_start: 0.8102 (pp) cc_final: 0.7747 (mt)
REVERT: A  411 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7568 (mm-30)
REVERT: B  125 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7437 (mp0)
REVERT: B  162 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7440 (mmp-170)
REVERT: B  372 THR cc_start: 0.8730 (p) cc_final: 0.8457 (m)
REVERT: B  424 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (tp40)
  outliers start: 40
  outliers final: 23
  residues processed: 240
  average time/residue: 0.5354
  time to fit residues: 138.2179
Evaluate side-chains
  237 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 210
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   25 SER
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  252 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  381 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 70 optimal weight:    0.1980
   chunk 108 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
K 164 ASN
A 133 GLN
B   8 GLN
B 165 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.133767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.107578 restraints weight = 31433.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.89
r_work: 0.3330 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10096  Z= 0.120
  Angle     :  0.545   7.078  13710  Z= 0.271
  Chirality :  0.044   0.206   1521
  Planarity :  0.004   0.046   1781
  Dihedral  :  9.052 148.525   1495
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.16 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.24), residues: 1231
  helix:  1.95 (0.23), residues: 516
  sheet:  0.94 (0.35), residues: 223
  loop : -0.69 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 103 
 TYR   0.011   0.001   TYR B 310 
 PHE   0.014   0.001   PHE K 182 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.003   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10096)
  covalent geometry    : angle       0.54483 (13710)
  hydrogen bonds       : bond        0.03839 (  479)
  hydrogen bonds       : angle       4.29177 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.318 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9002 (mt) cc_final: 0.8630 (tp)
REVERT: K  210 LYS cc_start: 0.7810 (tttt) cc_final: 0.7550 (mtpt)
REVERT: K  228 SER cc_start: 0.8462 (t) cc_final: 0.8182 (m)
REVERT: K  312 ILE cc_start: 0.8116 (mt) cc_final: 0.7902 (mm)
REVERT: K  402 MET cc_start: 0.8445 (ttm) cc_final: 0.8142 (ttt)
REVERT: A  411 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7264 (mm-30)
REVERT: A  429 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7586 (mt-10)
REVERT: A  431 ASP cc_start: 0.7919 (m-30) cc_final: 0.7701 (m-30)
REVERT: B  125 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: B  424 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8131 (tp40)
  outliers start: 32
  outliers final: 16
  residues processed: 226
  average time/residue: 0.5728
  time to fit residues: 139.2540
Evaluate side-chains
  223 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 GLN
B  48 ASN
B 426 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.130940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.104982 restraints weight = 30758.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.82
r_work: 0.3291 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  10096  Z= 0.243
  Angle     :  0.623   8.451  13710  Z= 0.314
  Chirality :  0.048   0.202   1521
  Planarity :  0.005   0.049   1781
  Dihedral  :  9.241 150.404   1495
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.34 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    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:  0.94 (0.24), residues: 1231
  helix:  1.84 (0.23), residues: 506
  sheet:  0.88 (0.35), residues: 224
  loop : -0.78 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 425 
 TYR   0.011   0.002   TYR B  59 
 PHE   0.017   0.002   PHE A 395 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.006   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (10096)
  covalent geometry    : angle       0.62308 (13710)
  hydrogen bonds       : bond        0.04840 (  479)
  hydrogen bonds       : angle       4.44204 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 205
  time to evaluate  : 0.410 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.8999 (mt) cc_final: 0.8637 (tp)
REVERT: K  113 MET cc_start: 0.7588 (tpt) cc_final: 0.7329 (tmm)
REVERT: K  210 LYS cc_start: 0.7865 (tttt) cc_final: 0.7621 (mtpt)
REVERT: K  228 SER cc_start: 0.8506 (t) cc_final: 0.8222 (m)
REVERT: K  402 MET cc_start: 0.8466 (ttm) cc_final: 0.8172 (ttt)
REVERT: A  431 ASP cc_start: 0.7916 (m-30) cc_final: 0.7709 (m-30)
REVERT: B  162 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7390 (mmp-170)
REVERT: B  282 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7590 (ttp-170)
REVERT: B  372 THR cc_start: 0.8660 (p) cc_final: 0.8385 (m)
REVERT: B  424 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8162 (tp40)
  outliers start: 35
  outliers final: 21
  residues processed: 220
  average time/residue: 0.5826
  time to fit residues: 137.6985
Evaluate side-chains
  226 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 202
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  173 VAL
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  282 ARG
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  415 MET
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 GLN
B 426 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.132596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.107324 restraints weight = 27614.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.63
r_work: 0.3331 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3330
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10096  Z= 0.152
  Angle     :  0.574   8.676  13710  Z= 0.287
  Chirality :  0.045   0.200   1521
  Planarity :  0.004   0.047   1781
  Dihedral  :  9.082 150.188   1495
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 19.65 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.24), residues: 1231
  helix:  1.94 (0.23), residues: 509
  sheet:  0.77 (0.35), residues: 226
  loop : -0.71 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 103 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.015   0.001   PHE K 182 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.004   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10096)
  covalent geometry    : angle       0.57426 (13710)
  hydrogen bonds       : bond        0.04216 (  479)
  hydrogen bonds       : angle       4.33723 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 0.386 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.9000 (mt) cc_final: 0.8644 (tp)
REVERT: K  113 MET cc_start: 0.7526 (tpt) cc_final: 0.7267 (tmm)
REVERT: K  228 SER cc_start: 0.8469 (t) cc_final: 0.8213 (m)
REVERT: K  402 MET cc_start: 0.8436 (ttm) cc_final: 0.8140 (ttt)
REVERT: A  431 ASP cc_start: 0.7909 (m-30) cc_final: 0.7684 (m-30)
REVERT: B  125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7327 (mp0)
REVERT: B  162 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7378 (mmp-170)
REVERT: B  372 THR cc_start: 0.8659 (p) cc_final: 0.8370 (m)
REVERT: B  424 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8107 (tp40)
  outliers start: 26
  outliers final: 16
  residues processed: 213
  average time/residue: 0.5696
  time to fit residues: 130.1563
Evaluate side-chains
  218 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  282 ILE
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  237 SER
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  328 GLU
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0370
   chunk 12 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 117 optimal weight:    0.6980
   overall best weight:    0.5636

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

Flipped N/Q/H residues before XYZ refinement:
** K 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN
A 133 GLN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.134593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.108442 restraints weight = 32355.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.94
r_work: 0.3341 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3342
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3342
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10096  Z= 0.111
  Angle     :  0.544   8.021  13710  Z= 0.270
  Chirality :  0.043   0.196   1521
  Planarity :  0.004   0.046   1781
  Dihedral  :  8.731 146.483   1494
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.02 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.25), residues: 1231
  helix:  2.04 (0.23), residues: 516
  sheet:  0.90 (0.36), residues: 223
  loop : -0.72 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K 425 
 TYR   0.010   0.001   TYR B 310 
 PHE   0.013   0.001   PHE K 182 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.003   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10096)
  covalent geometry    : angle       0.54384 (13710)
  hydrogen bonds       : bond        0.03619 (  479)
  hydrogen bonds       : angle       4.21115 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 0.314 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.8992 (mt) cc_final: 0.8660 (tp)
REVERT: K  228 SER cc_start: 0.8440 (t) cc_final: 0.8218 (m)
REVERT: K  402 MET cc_start: 0.8417 (ttm) cc_final: 0.8136 (ttt)
REVERT: A   36 MET cc_start: 0.8295 (ttt) cc_final: 0.7880 (ttt)
REVERT: A   60 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7761 (tttt)
REVERT: A  411 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7282 (mm-30)
REVERT: A  429 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7562 (mt-10)
REVERT: A  431 ASP cc_start: 0.7932 (m-30) cc_final: 0.7726 (m-30)
REVERT: B   73 MET cc_start: 0.8352 (mmp) cc_final: 0.8148 (mmt)
REVERT: B  108 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7508 (mp0)
REVERT: B  162 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7350 (mmp-170)
REVERT: B  197 ASP cc_start: 0.7873 (m-30) cc_final: 0.7561 (m-30)
REVERT: B  424 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8104 (tp40)
  outliers start: 22
  outliers final: 11
  residues processed: 227
  average time/residue: 0.5363
  time to fit residues: 131.1729
Evaluate side-chains
  228 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 213
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 133 GLN
B  52 ASN
B 195 ASN
B 347 ASN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.108240 restraints weight = 24177.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.49
r_work: 0.3357 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10096  Z= 0.139
  Angle     :  0.570   8.323  13710  Z= 0.283
  Chirality :  0.045   0.214   1521
  Planarity :  0.004   0.047   1781
  Dihedral  :  8.768 146.974   1494
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.58 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.24), residues: 1231
  helix:  2.01 (0.23), residues: 516
  sheet:  0.91 (0.35), residues: 223
  loop : -0.74 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG K 103 
 TYR   0.010   0.001   TYR B 310 
 PHE   0.014   0.001   PHE K 182 
 TRP   0.014   0.002   TRP A  21 
 HIS   0.005   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10096)
  covalent geometry    : angle       0.56979 (13710)
  hydrogen bonds       : bond        0.03953 (  479)
  hydrogen bonds       : angle       4.23845 ( 1354)

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

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

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2462 Ramachandran restraints generated.
    1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 207
  time to evaluate  : 0.401 
Fit side-chains
REVERT: K  106 ILE cc_start: 0.8984 (mt) cc_final: 0.8620 (tp)
REVERT: K  228 SER cc_start: 0.8510 (t) cc_final: 0.8288 (m)
REVERT: K  402 MET cc_start: 0.8504 (ttm) cc_final: 0.8228 (ttt)
REVERT: B  108 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7737 (mp0)
REVERT: B  162 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7456 (mmp-170)
REVERT: B  424 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (tp40)
  outliers start: 19
  outliers final: 12
  residues processed: 215
  average time/residue: 0.5588
  time to fit residues: 128.8883
Evaluate side-chains
  218 residues out of total 1070 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 203
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  165 THR
Chi-restraints excluded: chain K residue  198 THR
Chi-restraints excluded: chain K residue  325 THR
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue  108 GLU
Chi-restraints excluded: chain B residue  162 ARG
Chi-restraints excluded: chain B residue  238 THR
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  424 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 133 GLN
B  52 ASN
B 347 ASN
** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.133458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.108107 restraints weight = 25226.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.56
r_work: 0.3351 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3184
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3184 r_free = 0.3184    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3184
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10096  Z= 0.141
  Angle     :  0.573  10.872  13710  Z= 0.284
  Chirality :  0.045   0.204   1521
  Planarity :  0.004   0.047   1781
  Dihedral  :  8.773 147.425   1494
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 20.76 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1231
  helix:  1.99 (0.23), residues: 517
  sheet:  0.95 (0.35), residues: 227
  loop : -0.75 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 103 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.014   0.001   PHE K 182 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.005   0.001   HIS K 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10096)
  covalent geometry    : angle       0.57316 (13710)
  hydrogen bonds       : bond        0.03990 (  479)
  hydrogen bonds       : angle       4.24434 ( 1354)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4253.44 seconds
wall clock time: 73 minutes 10.25 seconds (4390.25 seconds total)