Starting phenix.real_space_refine
on Tue Jan 13 23:07:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqz_26076/01_2026/7tqz_26076.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      63      5.16       5
     C    6127      2.51       5
     N    1697      2.21       5
     O    1897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 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: 9790
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3437
          Classifications: {'peptide': 440}
          Link IDs: {'PTRANS': 20, 'TRANS': 419}
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3376
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 20, 'TRANS': 408}
    Chain: "K"
      Number of atoms: 2854
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 360, 2839
          Classifications: {'peptide': 360}
          Link IDs: {'PTRANS': 14, 'TRANS': 345}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 360, 2839
          Classifications: {'peptide': 360}
          Link IDs: {'PTRANS': 14, 'TRANS': 345}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2860
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'TA1': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.75, per 1000 atoms: 0.28
  Number of scatterers: 9790
  At special positions: 0
  Unit cell: (108.9, 72.6, 109.725, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P       5     15.00
     Mg      1     11.99
     O    1897      8.00
     N    1697      7.00
     C    6127      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: 0.82
  Conformation dependent library (CDL) restraints added in 602.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      49.1% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 29
    Processing helix  chain 'A' and resid 36 through 42
      removed outlier: 3.870A  pdb=" N   LYS A  40 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 102 through 108
      removed outlier: 3.665A  pdb=" N   GLY A 106 " --> pdb=" O   ASN A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 129
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 4.146A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 190
      removed outlier: 3.507A  pdb=" N   ASN A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 197
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.779A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 260
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 3.920A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.790A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.549A  pdb=" N   VAL A 328 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 400
      removed outlier: 4.038A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.822A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 435
      removed outlier: 4.065A  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 41 through 46
      removed outlier: 3.553A  pdb=" N   GLU B  45 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 41 through 46'
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 78
    Processing helix  chain 'B' and resid 81 through 85
    Processing helix  chain 'B' and resid 86 through 90
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 3.758A  pdb=" N   LEU B 112 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   SER B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.868A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   GLU B 194 " --> pdb=" O   HIS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
    Processing helix  chain 'B' and resid 221 through 237
      removed outlier: 3.688A  pdb=" N   THR B 237 " --> pdb=" O   MET B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 242
      removed outlier: 3.985A  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 285 through 295
    Processing helix  chain 'B' and resid 296 through 299
      removed outlier: 3.712A  pdb=" N   MET B 299 " --> pdb=" O   SER B 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 296 through 299'
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 322 through 337
    Processing helix  chain 'B' and resid 338 through 341
    Processing helix  chain 'B' and resid 373 through 390
      removed outlier: 4.121A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.570A  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: 3.735A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASP B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 48
      removed outlier: 4.189A  pdb=" N   LYS K  45 " --> pdb=" O   ASN K  41 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   ILE K  46 " --> pdb=" O   ARG K  42 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP K  47 " --> pdb=" O   LEU K  43 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 124 through 129
      removed outlier: 4.030A  pdb=" N   ARG K 129 " --> pdb=" O   THR K 125 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 157 through 164
      removed outlier: 3.778A  pdb=" N   ASN K 164 " --> pdb=" O   GLN K 160 " (cutoff:3.500A)
    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 274 through 288
      removed outlier: 3.623A  pdb=" N   ASN K 288 " --> pdb=" O   GLU K 284 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 339 through 343
    Processing helix  chain 'K' and resid 347 through 372
      removed outlier: 3.527A  pdb=" N   GLY K 353 " --> pdb=" O   ARG K 349 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA K 369 " --> pdb=" O   ASN K 365 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 373 through 378
      removed outlier: 4.156A  pdb=" N   ASN K 377 " --> pdb=" O   ARG K 374 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   HIS K 378 " --> pdb=" O   ARG K 375 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 380 through 383
      removed outlier: 3.845A  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 412 through 426
      removed outlier: 3.914A  pdb=" N   ALA K 426 " --> pdb=" O   TYR K 422 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93
      removed outlier: 7.920A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   PHE A  67 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 8.535A  pdb=" N   VAL A  66 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.088A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   GLU A   3 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   PHE A 135 " --> pdb=" O   GLU A   3 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ILE A   5 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A   5 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   VAL A   9 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   SER A 165 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   HIS A 139 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LYS A 166 " --> pdb=" O   CYS A 200 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   PHE A 202 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   GLU A 168 " --> pdb=" O   PHE A 202 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   VAL A 204 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   SER A 170 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272
    Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 66
      removed outlier: 5.650A  pdb=" N   GLU B   3 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLY B 132 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   SER B 138 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.926A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.748A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 7.357A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54
    Processing sheet with id=AA6, first strand: chain 'K' and resid 150 through 152
      removed outlier: 6.448A  pdb=" N   THR K 180 " --> pdb=" O   VAL K 401 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   ILE K 403 " --> pdb=" O   THR K 180 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   PHE K 182 " --> pdb=" O   ILE K 403 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   CYS K 405 " --> pdb=" O   PHE K 182 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TYR K 184 " --> pdb=" O   CYS K 405 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ALA K 179 " --> pdb=" O   SER K 330 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   ILE K 332 " --> pdb=" O   ALA K 179 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL K 181 " --> pdb=" O   ILE K 332 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   LEU K 334 " --> pdb=" O   VAL K 181 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ALA K 183 " --> pdb=" O   LEU K 334 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 106 through 110
      removed outlier: 5.173A  pdb=" N   VAL K 108 " --> pdb=" O   ILE K 115 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ILE K 115 " --> pdb=" O   VAL K 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 291 through 294
      removed outlier: 6.308A  pdb=" N   SER K 292 " --> pdb=" O   THR K 299 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   THR K 299 " --> pdb=" O   SER K 292 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1326 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: 1.06 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: 1728
        1.32 -     1.45: 2580
        1.45 -     1.57: 5576
        1.57 -     1.69: 12
        1.69 -     1.82: 98
  Bond restraints: 9994
  Sorted by residual:
  bond pdb=" N   ILE K 105 "
       pdb=" CA  ILE K 105 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.22e-02 6.72e+03 7.83e+00
  bond pdb=" N   VAL B 169 "
       pdb=" CA  VAL B 169 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.034 1.23e-02 6.61e+03 7.43e+00
  bond pdb=" N   CYS K 291 "
       pdb=" CA  CYS K 291 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.73e+00
  bond pdb=" C   SER K 407 "
       pdb=" N   PRO K 408 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 8.90e-03 1.26e+04 6.58e+00
  bond pdb=" N   VAL K  44 "
       pdb=" CA  VAL K  44 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 1.26e-02 6.30e+03 6.37e+00
  ... (remaining 9989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 13273
        2.42 -     4.83: 246
        4.83 -     7.25: 42
        7.25 -     9.67: 2
        9.67 -    12.09: 3
  Bond angle restraints: 13566
  Sorted by residual:
  angle pdb=" C   GLU K 295 "
        pdb=" CA  GLU K 295 "
        pdb=" CB  GLU K 295 "
      ideal   model   delta    sigma   weight residual
     116.54  110.33    6.21 1.15e+00 7.56e-01 2.91e+01
  angle pdb=" C19 TA1 B 502 "
        pdb=" C18 TA1 B 502 "
        pdb=" C20 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     112.17  100.08   12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" C14 TA1 B 502 "
        pdb=" C11 TA1 B 502 "
        pdb=" O04 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     119.42  107.44   11.98 3.00e+00 1.11e-01 1.59e+01
  angle pdb=" C10 TA1 B 502 "
        pdb=" C18 TA1 B 502 "
        pdb=" C20 TA1 B 502 "
      ideal   model   delta    sigma   weight residual
     104.78  116.29  -11.51 3.00e+00 1.11e-01 1.47e+01
  angle pdb=" CA  ASN K 377 "
        pdb=" CB  ASN K 377 "
        pdb=" CG  ASN K 377 "
      ideal   model   delta    sigma   weight residual
     112.60  116.04   -3.44 1.00e+00 1.00e+00 1.19e+01
  ... (remaining 13561 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.86: 5847
       29.86 -    59.73: 209
       59.73 -    89.59: 22
       89.59 -   119.45: 9
      119.45 -   149.32: 12
  Dihedral angle restraints: 6099
    sinusoidal: 2531
      harmonic: 3568
  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  -44.72  149.32     1      2.00e+01 2.50e-03 4.46e+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 -168.26 -122.47     1      2.00e+01 2.50e-03 3.69e+01
  dihedral pdb=" CA  ALA B  54 "
           pdb=" C   ALA B  54 "
           pdb=" N   THR B  55 "
           pdb=" CA  THR B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.03  -28.97     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 6096 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.108: 1429
       0.108 -    0.215: 77
       0.215 -    0.323: 0
       0.323 -    0.430: 0
       0.430 -    0.538: 1
  Chirality restraints: 1507
  Sorted by residual:
  chirality pdb=" C18 TA1 B 502 "
            pdb=" C10 TA1 B 502 "
            pdb=" C17 TA1 B 502 "
            pdb=" C20 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -3.16   -2.62   -0.54 2.00e-01 2.50e+01 7.24e+00
  chirality pdb=" C02 TA1 B 502 "
            pdb=" C01 TA1 B 502 "
            pdb=" C10 TA1 B 502 "
            pdb=" O02 TA1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.56    2.77   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  ILE K 105 "
            pdb=" N   ILE K 105 "
            pdb=" C   ILE K 105 "
            pdb=" CB  ILE K 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.17e-01
  ... (remaining 1504 not shown)

  Planarity restraints: 1767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  57 "   -0.013 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   ASN B  57 "    0.047 2.00e-02 2.50e+03
        pdb=" O   ASN B  57 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LYS B  58 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 383 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   GLU B 383 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B 383 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN B 384 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN K 418 "   -0.009 2.00e-02 2.50e+03   1.86e-02 3.46e+00
        pdb=" C   ASN K 418 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ASN K 418 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   THR K 419 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1764 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 100
        2.61 -     3.18: 8409
        3.18 -     3.75: 14793
        3.75 -     4.33: 20979
        4.33 -     4.90: 35843
  Nonbonded interactions: 80124
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  69 "
            pdb="MG    MG A 502 "
     model   vdw
     2.035 2.170
  nonbonded pdb=" OG  SER B 172 "
            pdb=" OD1 ASP B 203 "
     model   vdw
     2.036 3.040
  nonbonded pdb=" O   ASN B 226 "
            pdb=" OG  SER B 230 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" O   GLU A  71 "
            pdb="MG    MG A 502 "
     model   vdw
     2.120 2.170
  nonbonded pdb=" O   SER K 263 "
            pdb=" OG  SER K 263 "
     model   vdw
     2.218 3.040
  ... (remaining 80119 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=0.42 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:             5.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.860
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9994  Z= 0.257
  Angle     :  0.792  12.087  13566  Z= 0.437
  Chirality :  0.050   0.538   1507
  Planarity :  0.005   0.056   1767
  Dihedral  : 17.394 149.316   3803
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 12.66 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.24), residues: 1223
  helix:  1.04 (0.23), residues: 501
  sheet: -0.50 (0.36), residues: 211
  loop : -1.05 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 142 
 TYR   0.020   0.001   TYR A 172 
 PHE   0.018   0.001   PHE B 212 
 TRP   0.016   0.002   TRP A 388 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9994)
  covalent geometry    : angle       0.79226 (13566)
  hydrogen bonds       : bond        0.15672 (  466)
  hydrogen bonds       : angle       6.37654 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 189
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: B  306 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8283 (mtm180)
REVERT: B  423 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8093 (tm-30)
REVERT: K  161 VAL cc_start: 0.8439 (t) cc_final: 0.8227 (p)
REVERT: K  402 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (ttt)
  outliers start: 9
  outliers final: 8
  residues processed: 196
  average time/residue: 0.5830
  time to fit residues: 122.3037
Evaluate side-chains
  183 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 174
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain B residue  304 ASP
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue  228 SER
Chi-restraints excluded: chain K residue  249 CYS
Chi-restraints excluded: chain K residue  326 PHE
Chi-restraints excluded: chain K residue  402 MET
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
A 107 HIS
B   6 HIS
B 100 ASN
B 134 GLN
B 291 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.116918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.093230 restraints weight = 20981.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.71
r_work: 0.3207 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9994  Z= 0.145
  Angle     :  0.593  10.876  13566  Z= 0.289
  Chirality :  0.044   0.263   1507
  Planarity :  0.004   0.036   1767
  Dihedral  : 11.573 145.707   1492
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.05 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.63 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.25), residues: 1223
  helix:  1.64 (0.24), residues: 509
  sheet: -0.32 (0.36), residues: 213
  loop : -0.85 (0.27), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 145 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.011   0.001   PHE A 149 
 TRP   0.012   0.002   TRP A  21 
 HIS   0.004   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9994)
  covalent geometry    : angle       0.59301 (13566)
  hydrogen bonds       : bond        0.04755 (  466)
  hydrogen bonds       : angle       4.62632 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 175
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A    2 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6957 (pmt-80)
REVERT: A   75 ILE cc_start: 0.7990 (mm) cc_final: 0.7756 (mp)
REVERT: A  203 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8612 (mtp)
REVERT: A  254 GLU cc_start: 0.8000 (mt-10) cc_final: 0.6934 (mm-30)
REVERT: A  398 MET cc_start: 0.8516 (mtm) cc_final: 0.8176 (mtp)
REVERT: B   57 ASN cc_start: 0.7595 (t0) cc_final: 0.7286 (t0)
REVERT: B  195 ASN cc_start: 0.8752 (m-40) cc_final: 0.8468 (m110)
REVERT: B  288 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7790 (mm-30)
REVERT: B  291 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: B  306 ARG cc_start: 0.8663 (mtm180) cc_final: 0.8403 (mtm180)
REVERT: B  423 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8182 (tm-30)
REVERT: K  161 VAL cc_start: 0.8506 (t) cc_final: 0.8278 (p)
  outliers start: 26
  outliers final: 13
  residues processed: 187
  average time/residue: 0.5942
  time to fit residues: 118.6837
Evaluate side-chains
  178 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  115 ILE
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  156 CYS
Chi-restraints excluded: chain K residue  350 LEU
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 71 optimal weight:    0.1980
   chunk 117 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 108 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   chunk 119 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
B  14 ASN
B 204 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.112245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.088400 restraints weight = 23812.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.85
r_work: 0.3119 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   9994  Z= 0.299
  Angle     :  0.651   8.365  13566  Z= 0.323
  Chirality :  0.049   0.456   1507
  Planarity :  0.004   0.043   1767
  Dihedral  :  8.963 147.908   1479
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.69 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 12.10 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.24), residues: 1223
  helix:  1.52 (0.24), residues: 508
  sheet: -0.11 (0.35), residues: 213
  loop : -0.95 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 302 
 TYR   0.014   0.002   TYR B 222 
 PHE   0.017   0.002   PHE A 255 
 TRP   0.015   0.002   TRP A  21 
 HIS   0.006   0.002   HIS B 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00728 ( 9994)
  covalent geometry    : angle       0.65109 (13566)
  hydrogen bonds       : bond        0.05555 (  466)
  hydrogen bonds       : angle       4.66707 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 176
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  203 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8713 (mtt)
REVERT: A  377 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7616 (tpt)
REVERT: A  424 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.8010 (m-30)
REVERT: B   57 ASN cc_start: 0.8105 (t0) cc_final: 0.7884 (t0)
REVERT: B  195 ASN cc_start: 0.8830 (m-40) cc_final: 0.8525 (m110)
REVERT: B  288 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7825 (mm-30)
REVERT: B  291 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: B  306 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8441 (mtm180)
REVERT: B  406 MET cc_start: 0.8359 (tpp) cc_final: 0.8034 (tpt)
REVERT: K  161 VAL cc_start: 0.8634 (t) cc_final: 0.8417 (p)
  outliers start: 38
  outliers final: 16
  residues processed: 197
  average time/residue: 0.6198
  time to fit residues: 130.4204
Evaluate side-chains
  190 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 171
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  424 ASP
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  156 CYS
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 110 optimal weight:    0.4980
   chunk 118 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
B 100 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.116221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.092664 restraints weight = 21966.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.77
r_work: 0.3193 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9994  Z= 0.122
  Angle     :  0.545   9.982  13566  Z= 0.268
  Chirality :  0.044   0.340   1507
  Planarity :  0.004   0.037   1767
  Dihedral  :  8.276 143.934   1479
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.54 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.20 %
    Favored  : 82.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.24), residues: 1223
  helix:  1.69 (0.24), residues: 512
  sheet:  0.15 (0.36), residues: 203
  loop : -0.98 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 145 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.010   0.001   PHE B 367 
 TRP   0.013   0.002   TRP A  21 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9994)
  covalent geometry    : angle       0.54481 (13566)
  hydrogen bonds       : bond        0.04068 (  466)
  hydrogen bonds       : angle       4.35932 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.8013 (mt-10) cc_final: 0.6863 (mm-30)
REVERT: A  377 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7504 (tpt)
REVERT: A  398 MET cc_start: 0.8570 (mtm) cc_final: 0.8335 (mtp)
REVERT: B   57 ASN cc_start: 0.8065 (t0) cc_final: 0.7858 (t0)
REVERT: B  158 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8463 (tt0)
REVERT: B  195 ASN cc_start: 0.8756 (m-40) cc_final: 0.8434 (m110)
REVERT: B  288 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7767 (mm-30)
REVERT: B  291 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7785 (tm-30)
REVERT: B  306 ARG cc_start: 0.8707 (mtm180) cc_final: 0.8416 (mtm180)
REVERT: B  406 MET cc_start: 0.8186 (tpp) cc_final: 0.7874 (tpt)
REVERT: B  423 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8321 (tm-30)
REVERT: K  127 MET cc_start: -0.0834 (pmt) cc_final: -0.1242 (pmm)
REVERT: K  161 VAL cc_start: 0.8596 (t) cc_final: 0.8392 (p)
  outliers start: 25
  outliers final: 12
  residues processed: 191
  average time/residue: 0.5803
  time to fit residues: 118.6437
Evaluate side-chains
  175 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  156 CYS
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 62 optimal weight:    0.4980
   chunk 108 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
B 131 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.116117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.091744 restraints weight = 28939.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.17
r_work: 0.3161 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9994  Z= 0.127
  Angle     :  0.538   8.508  13566  Z= 0.264
  Chirality :  0.044   0.280   1507
  Planarity :  0.004   0.037   1767
  Dihedral  :  7.867 140.369   1479
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.70 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.38 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.24), residues: 1223
  helix:  1.76 (0.24), residues: 512
  sheet:  0.25 (0.37), residues: 203
  loop : -0.93 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 320 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.011   0.001   PHE B 367 
 TRP   0.013   0.001   TRP A  21 
 HIS   0.002   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 9994)
  covalent geometry    : angle       0.53843 (13566)
  hydrogen bonds       : bond        0.04011 (  466)
  hydrogen bonds       : angle       4.29158 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 169
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  203 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8669 (mtp)
REVERT: A  254 GLU cc_start: 0.8031 (mt-10) cc_final: 0.6730 (mm-30)
REVERT: A  377 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7574 (tpt)
REVERT: A  398 MET cc_start: 0.8574 (mtm) cc_final: 0.8353 (mtp)
REVERT: B   46 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8330 (mmp80)
REVERT: B  158 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (tt0)
REVERT: B  195 ASN cc_start: 0.8690 (m-40) cc_final: 0.8386 (m110)
REVERT: B  288 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7785 (mm-30)
REVERT: B  291 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: B  297 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8574 (mmtt)
REVERT: B  306 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8429 (mtm180)
REVERT: B  406 MET cc_start: 0.8201 (tpp) cc_final: 0.7883 (tpt)
REVERT: B  423 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8386 (tm-30)
REVERT: K  127 MET cc_start: -0.0721 (pmt) cc_final: -0.1157 (pmm)
  outliers start: 26
  outliers final: 13
  residues processed: 183
  average time/residue: 0.5950
  time to fit residues: 116.4513
Evaluate side-chains
  175 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  293 MET
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  423 GLN
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  350 LEU
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 4 optimal weight:    0.0070
   chunk 55 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 103 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
A 258 ASN
** K 107 ASN ** 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 = 0.3711 r_free = 0.3711 target = 0.117568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.094888 restraints weight = 17744.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.45
r_work: 0.3242 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9994  Z= 0.107
  Angle     :  0.522   7.326  13566  Z= 0.259
  Chirality :  0.043   0.241   1507
  Planarity :  0.003   0.038   1767
  Dihedral  :  7.573 136.726   1479
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.78 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.85 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.24), residues: 1223
  helix:  1.81 (0.23), residues: 515
  sheet:  0.34 (0.37), residues: 203
  loop : -0.91 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 346 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.010   0.001   PHE B 367 
 TRP   0.011   0.001   TRP A  21 
 HIS   0.003   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9994)
  covalent geometry    : angle       0.52246 (13566)
  hydrogen bonds       : bond        0.03662 (  466)
  hydrogen bonds       : angle       4.23132 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  203 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8784 (mtp)
REVERT: A  254 GLU cc_start: 0.8088 (mt-10) cc_final: 0.6911 (mm-30)
REVERT: A  337 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8617 (p)
REVERT: A  377 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7714 (tpt)
REVERT: B  158 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8633 (tt0)
REVERT: B  195 ASN cc_start: 0.8759 (m-40) cc_final: 0.8461 (m110)
REVERT: B  288 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7947 (mm-30)
REVERT: B  291 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: B  297 LYS cc_start: 0.9154 (ptmt) cc_final: 0.8580 (mmtt)
REVERT: B  306 ARG cc_start: 0.8844 (mtm180) cc_final: 0.8549 (mtm180)
REVERT: B  406 MET cc_start: 0.8299 (tpp) cc_final: 0.8011 (tpt)
REVERT: B  423 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8474 (tm-30)
REVERT: K  127 MET cc_start: -0.0747 (pmt) cc_final: -0.1173 (pmm)
  outliers start: 26
  outliers final: 11
  residues processed: 187
  average time/residue: 0.5705
  time to fit residues: 114.4017
Evaluate side-chains
  180 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  423 GLN
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  149 ASP
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   chunk 112 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0970
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
B 424 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.112905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.088499 restraints weight = 29981.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 3.17
r_work: 0.3103 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   9994  Z= 0.270
  Angle     :  0.635  12.766  13566  Z= 0.315
  Chirality :  0.047   0.238   1507
  Planarity :  0.004   0.043   1767
  Dihedral  :  8.029 143.430   1479
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.28 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.04 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.24), residues: 1223
  helix:  1.75 (0.24), residues: 504
  sheet:  0.32 (0.37), residues: 203
  loop : -0.92 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 346 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.016   0.002   PHE A 255 
 TRP   0.010   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00660 ( 9994)
  covalent geometry    : angle       0.63512 (13566)
  hydrogen bonds       : bond        0.05021 (  466)
  hydrogen bonds       : angle       4.48281 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 179
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.8038 (mt-10) cc_final: 0.6993 (mm-30)
REVERT: A  337 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8617 (p)
REVERT: A  377 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7653 (tpt)
REVERT: B    1 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8538 (ttm)
REVERT: B   46 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8309 (mmp80)
REVERT: B  158 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8479 (tt0)
REVERT: B  194 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8372 (mm-30)
REVERT: B  195 ASN cc_start: 0.8798 (m-40) cc_final: 0.8488 (m110)
REVERT: B  288 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7832 (mm-30)
REVERT: B  291 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7849 (tm-30)
REVERT: B  297 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8776 (ptmt)
REVERT: B  306 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8462 (mtm180)
REVERT: B  406 MET cc_start: 0.8355 (tpp) cc_final: 0.8057 (tpt)
REVERT: K  127 MET cc_start: -0.0772 (pmt) cc_final: -0.1125 (pmm)
  outliers start: 33
  outliers final: 19
  residues processed: 196
  average time/residue: 0.5925
  time to fit residues: 124.0733
Evaluate side-chains
  200 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  194 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  109 VAL
Chi-restraints excluded: chain K residue  151 LEU
Chi-restraints excluded: chain K residue  156 CYS
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 117 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B   8 GLN
B 100 ASN
B 348 ASN
B 424 GLN
** K 107 ASN ** 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 = 0.3703 r_free = 0.3703 target = 0.116863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.092411 restraints weight = 29233.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.19
r_work: 0.3169 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9994  Z= 0.115
  Angle     :  0.541   8.268  13566  Z= 0.270
  Chirality :  0.043   0.211   1507
  Planarity :  0.004   0.038   1767
  Dihedral  :  7.625 139.108   1479
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.54 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.79 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.24), residues: 1223
  helix:  1.81 (0.24), residues: 512
  sheet:  0.41 (0.37), residues: 203
  loop : -0.90 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG K 346 
 TYR   0.010   0.001   TYR A 103 
 PHE   0.010   0.001   PHE A 149 
 TRP   0.014   0.002   TRP A 388 
 HIS   0.002   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9994)
  covalent geometry    : angle       0.54146 (13566)
  hydrogen bonds       : bond        0.03767 (  466)
  hydrogen bonds       : angle       4.26974 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.7991 (mt-10) cc_final: 0.6855 (mm-30)
REVERT: A  337 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8593 (p)
REVERT: A  377 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7551 (tpt)
REVERT: B    1 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8500 (ttm)
REVERT: B  158 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8479 (tt0)
REVERT: B  195 ASN cc_start: 0.8671 (m-40) cc_final: 0.8370 (m110)
REVERT: B  288 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: B  291 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: B  297 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8579 (mmtt)
REVERT: B  306 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8436 (mtm180)
REVERT: B  406 MET cc_start: 0.8231 (tpp) cc_final: 0.7923 (tpt)
REVERT: B  423 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8275 (tm-30)
REVERT: K  127 MET cc_start: -0.0849 (pmt) cc_final: -0.1223 (pmm)
REVERT: K  350 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8141 (tp)
REVERT: K  397 ASN cc_start: 0.8044 (m-40) cc_final: 0.7785 (p0)
  outliers start: 28
  outliers final: 14
  residues processed: 192
  average time/residue: 0.5765
  time to fit residues: 118.6301
Evaluate side-chains
  187 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 167
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  296 SER
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  354 CYS
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  350 LEU
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
B 424 GLN
** K 107 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.116626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.092388 restraints weight = 27889.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 3.08
r_work: 0.3177 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3177
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3177 r_free = 0.3177    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3177
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9994  Z= 0.126
  Angle     :  0.556   7.514  13566  Z= 0.278
  Chirality :  0.043   0.208   1507
  Planarity :  0.004   0.038   1767
  Dihedral  :  7.531 137.193   1479
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.78 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.92 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.24), residues: 1223
  helix:  1.82 (0.23), residues: 514
  sheet:  0.46 (0.37), residues: 203
  loop : -0.86 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 320 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.011   0.001   PHE A 149 
 TRP   0.017   0.002   TRP A 388 
 HIS   0.002   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9994)
  covalent geometry    : angle       0.55560 (13566)
  hydrogen bonds       : bond        0.03848 (  466)
  hydrogen bonds       : angle       4.26502 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.7971 (mt-10) cc_final: 0.6868 (mm-30)
REVERT: A  337 THR cc_start: 0.9044 (OUTLIER) cc_final: 0.8621 (p)
REVERT: A  377 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7563 (tpt)
REVERT: B  158 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8462 (tt0)
REVERT: B  164 MET cc_start: 0.8430 (tpp) cc_final: 0.8199 (tpt)
REVERT: B  195 ASN cc_start: 0.8677 (m-40) cc_final: 0.8374 (m110)
REVERT: B  288 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7734 (mm-30)
REVERT: B  291 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: B  297 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8584 (mmtt)
REVERT: B  306 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8438 (mtm180)
REVERT: B  406 MET cc_start: 0.8215 (tpp) cc_final: 0.7926 (tpt)
REVERT: B  423 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8278 (tm-30)
REVERT: K  127 MET cc_start: -0.0878 (pmt) cc_final: -0.1194 (pmm)
REVERT: K  359 SER cc_start: 0.8887 (t) cc_final: 0.8665 (m)
REVERT: K  397 ASN cc_start: 0.8009 (m-40) cc_final: 0.7774 (p0)
  outliers start: 22
  outliers final: 13
  residues processed: 184
  average time/residue: 0.5561
  time to fit residues: 109.9798
Evaluate side-chains
  187 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  354 CYS
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.1980
   chunk 103 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 119 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 88 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 348 ASN
B 424 GLN
** K 107 ASN ** 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 = 0.3701 r_free = 0.3701 target = 0.116738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.092833 restraints weight = 25656.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.98
r_work: 0.3189 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9994  Z= 0.131
  Angle     :  0.555   8.386  13566  Z= 0.276
  Chirality :  0.043   0.202   1507
  Planarity :  0.004   0.038   1767
  Dihedral  :  7.487 136.205   1479
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.62 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.57 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.24), residues: 1223
  helix:  1.82 (0.23), residues: 515
  sheet:  0.46 (0.37), residues: 203
  loop : -0.85 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 320 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.011   0.001   PHE A 149 
 TRP   0.016   0.002   TRP A 388 
 HIS   0.002   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9994)
  covalent geometry    : angle       0.55469 (13566)
  hydrogen bonds       : bond        0.03847 (  466)
  hydrogen bonds       : angle       4.25101 ( 1326)

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

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

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

  2446 Ramachandran restraints generated.
    1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A   55 GLU cc_start: 0.7677 (tp30) cc_final: 0.7467 (tp30)
REVERT: A  254 GLU cc_start: 0.7963 (mt-10) cc_final: 0.6865 (mm-30)
REVERT: A  337 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8620 (p)
REVERT: A  377 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7543 (tpt)
REVERT: B  158 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8483 (tt0)
REVERT: B  195 ASN cc_start: 0.8682 (m-40) cc_final: 0.8378 (m110)
REVERT: B  288 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7743 (mm-30)
REVERT: B  291 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7750 (tm-30)
REVERT: B  297 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8580 (mmtt)
REVERT: B  306 ARG cc_start: 0.8714 (mtm180) cc_final: 0.8415 (mtm180)
REVERT: B  406 MET cc_start: 0.8215 (tpp) cc_final: 0.7928 (tpt)
REVERT: B  423 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8271 (tm-30)
REVERT: K  127 MET cc_start: -0.0957 (pmt) cc_final: -0.1273 (pmm)
REVERT: K  359 SER cc_start: 0.8879 (t) cc_final: 0.8659 (m)
REVERT: K  397 ASN cc_start: 0.8012 (m-40) cc_final: 0.7787 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 176
  average time/residue: 0.5793
  time to fit residues: 109.1203
Evaluate side-chains
  185 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 ARG
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  271 THR
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  377 MET
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   78 SER
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  297 LYS
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  354 CYS
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain K residue  181 VAL
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  417 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0980
   chunk 9 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 424 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.117024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.092934 restraints weight = 25361.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.97
r_work: 0.3188 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9994  Z= 0.129
  Angle     :  0.577  15.565  13566  Z= 0.283
  Chirality :  0.043   0.200   1507
  Planarity :  0.004   0.053   1767
  Dihedral  :  7.421 135.026   1479
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.57 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.24), residues: 1223
  helix:  1.80 (0.23), residues: 515
  sheet:  0.45 (0.37), residues: 203
  loop : -0.83 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 390 
 TYR   0.011   0.001   TYR A 103 
 PHE   0.010   0.001   PHE A 149 
 TRP   0.017   0.002   TRP A 388 
 HIS   0.002   0.001   HIS B 396 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9994)
  covalent geometry    : angle       0.57720 (13566)
  hydrogen bonds       : bond        0.03811 (  466)
  hydrogen bonds       : angle       4.26762 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3758.59 seconds
wall clock time: 64 minutes 50.01 seconds (3890.01 seconds total)