Starting phenix.real_space_refine
on Tue Jan 13 23:14:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tr1_26078/01_2026/7tr1_26078.map"
  }
  resolution = 3.1
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      2      5.21       5
     S      62      5.16       5
     C    6063      2.51       5
     N    1680      2.21       5
     O    1892      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 9707
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "K"
      Number of atoms: 2730
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 346, 2722
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 10, 'TRANS': 335}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 346, 2722
          Classifications: {'peptide': 346}
          Link IDs: {'PTRANS': 10, 'TRANS': 335}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 2746
    Chain: "A"
      Number of atoms: 3446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3446
          Classifications: {'peptide': 441}
          Link IDs: {'PTRANS': 20, 'TRANS': 420}
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3376
          Classifications: {'peptide': 429}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408}
    Chain: "K"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    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: 2.79, per 1000 atoms: 0.29
  Number of scatterers: 9707
  At special positions: 0
  Unit cell: (112.27, 77.39, 113.36, 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      62     16.00
     P       8     15.00
     Mg      2     11.99
     O    1892      8.00
     N    1680      7.00
     C    6063      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: 0.85
  Conformation dependent library (CDL) restraints added in 551.5 milliseconds
  

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 9 sheets defined
      48.7% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'K' and resid 36 through 46
      removed outlier: 3.543A  pdb=" N   ARG K  42 " --> pdb=" O   ALA K  38 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 46 through 51
      removed outlier: 4.250A  pdb=" N   ASP K  50 " --> pdb=" O   ILE K  46 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 157 through 166
    Processing helix  chain 'K' and resid 166 through 175
    Processing helix  chain 'K' and resid 191 through 196
      removed outlier: 3.526A  pdb=" N   SER K 196 " --> pdb=" O   THR K 192 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 203 through 220
    Processing helix  chain 'K' and resid 274 through 289
    Processing helix  chain 'K' and resid 339 through 343
    Processing helix  chain 'K' and resid 347 through 372
      removed outlier: 3.851A  pdb=" N   ASN K 351 " --> pdb=" O   GLY K 347 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 380 through 383
      removed outlier: 3.833A  pdb=" N   ASP K 383 " --> pdb=" O   PRO K 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 380 through 383'
    Processing helix  chain 'K' and resid 384 through 390
    Processing helix  chain 'K' and resid 390 through 395
      removed outlier: 3.992A  pdb=" N   GLY K 395 " --> pdb=" O   LYS K 391 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 413 through 427
    Processing helix  chain 'A' and resid 10 through 29
      removed outlier: 3.736A  pdb=" N   ALA A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 41
      removed outlier: 3.799A  pdb=" N   ASP A  39 " --> pdb=" O   MET A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 81
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.524A  pdb=" N   VAL A 118 " --> pdb=" O   ILE A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 161
      removed outlier: 4.081A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 194
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 3.815A  pdb=" N   LEU A 227 " --> pdb=" O   THR A 223 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 260
      removed outlier: 4.258A  pdb=" N   GLN A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR A 257 " --> pdb=" O   THR A 253 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN A 258 " --> pdb=" O   GLU A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 282
      removed outlier: 4.180A  pdb=" N   TYR A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 3.657A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 324 through 338
      removed outlier: 3.535A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 401
      removed outlier: 3.948A  pdb=" N   ALA A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A 397 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   MET A 398 " --> pdb=" O   LYS A 394 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
    Processing helix  chain 'A' and resid 415 through 435
      removed outlier: 3.824A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   MET A 425 " --> pdb=" O   ALA A 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 29
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.335A  pdb=" N   ARG B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 49
      No H-bonds generated for 'chain 'B' and resid 47 through 49'
    Processing helix  chain 'B' and resid 70 through 79
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 100 through 106
    Processing helix  chain 'B' and resid 108 through 111
    Processing helix  chain 'B' and resid 112 through 126
      removed outlier: 3.582A  pdb=" N   VAL B 116 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   SER B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 159
      removed outlier: 4.186A  pdb=" N   THR B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 196
      removed outlier: 3.801A  pdb=" N   GLN B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
      removed outlier: 4.190A  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 234
      removed outlier: 3.593A  pdb=" N   LEU B 225 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR B 232 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 241
    Processing helix  chain 'B' and resid 249 through 256
    Processing helix  chain 'B' and resid 285 through 295
    Processing helix  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: 4.144A  pdb=" N   LEU B 377 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE B 378 " --> pdb=" O   ILE B 374 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR B 386 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   MET B 388 " --> pdb=" O   GLN B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 404 through 427
      removed outlier: 3.901A  pdb=" N   PHE B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP B 427 " --> pdb=" O   GLN B 423 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 23 through 25
      removed outlier: 3.996A  pdb=" N   THR K 431 " --> pdb=" O   SER K  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 27 through 32
      removed outlier: 3.721A  pdb=" N   LYS K 399 " --> pdb=" O   ASN K 178 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA K 179 " --> pdb=" O   THR K 328 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER K 330 " --> pdb=" O   ALA K 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 113 through 115
    Processing sheet with id=AA4, first strand: chain 'K' and resid 254 through 256
    Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93
      removed outlier: 7.776A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE A  67 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ILE A 171 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   CYS A 200 " --> pdb=" O   LYS A 166 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 272
      removed outlier: 6.607A  pdb=" N   ALA A 374 " --> pdb=" O   TYR A 319 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   TYR A 319 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   CYS A 376 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   LEU A 317 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 315 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   CYS A 315 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ASN A 380 " --> pdb=" O   MET A 313 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92
      removed outlier: 8.151A  pdb=" N   VAL B  91 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   LEU B  65 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 8.646A  pdb=" N   ILE B  64 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  64 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   VAL B  66 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   GLN B   8 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   GLU B   3 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   PHE B 133 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   VAL B   5 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   LEU B 135 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   HIS B 137 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 7.597A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS B 137 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR B 199 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   CYS B 201 " --> pdb=" O   PRO B 268 " (cutoff:3.500A)
      removed outlier: 10.509A  pdb=" N   PHE B 270 " --> pdb=" O   CYS B 201 " (cutoff:3.500A)
      removed outlier: 13.802A  pdb=" N   ASP B 203 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   PHE B 265 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   SER B 371 " --> pdb=" O   PHE B 265 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   SER B 364 " --> pdb=" O   PHE B 317 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   PHE B 317 " --> pdb=" O   SER B 364 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   THR B 366 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA B 315 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ILE B 368 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   VAL B 313 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASN B 370 " --> pdb=" O   LEU B 311 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 51 through 53

    443 hydrogen bonds defined for protein.
    1253 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: 1.65

  Time building geometry restraints manager: 1.11 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: 1777
        1.32 -     1.45: 2497
        1.45 -     1.57: 5516
        1.57 -     1.69: 16
        1.69 -     1.82: 98
  Bond restraints: 9904
  Sorted by residual:
  bond pdb=" O3A ANP K 502 "
       pdb=" PB  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.700  1.584  0.116 2.00e-02 2.50e+03 3.39e+01
  bond pdb=" C4  ANP K 502 "
       pdb=" C5  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.387  1.463 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" N3B ANP K 502 "
       pdb=" PG  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.795  1.721  0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C5  ANP K 502 "
       pdb=" C6  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.405  1.470 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" N3B ANP K 502 "
       pdb=" PB  ANP K 502 "
    ideal  model  delta    sigma   weight residual
    1.669  1.726 -0.057 2.00e-02 2.50e+03 8.03e+00
  ... (remaining 9899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.02: 13276
        3.02 -     6.04: 160
        6.04 -     9.06: 12
        9.06 -    12.07: 1
       12.07 -    15.09: 1
  Bond angle restraints: 13450
  Sorted by residual:
  angle pdb=" N   LYS K 191 "
        pdb=" CA  LYS K 191 "
        pdb=" C   LYS K 191 "
      ideal   model   delta    sigma   weight residual
     113.41  106.90    6.51 1.22e+00 6.72e-01 2.85e+01
  angle pdb=" PB  ANP K 502 "
        pdb=" N3B ANP K 502 "
        pdb=" PG  ANP K 502 "
      ideal   model   delta    sigma   weight residual
     126.95  111.86   15.09 3.00e+00 1.11e-01 2.53e+01
  angle pdb=" C   ARG K  33 "
        pdb=" N   PRO K  34 "
        pdb=" CA  PRO K  34 "
      ideal   model   delta    sigma   weight residual
     120.66  125.06   -4.40 1.09e+00 8.42e-01 1.63e+01
  angle pdb=" PA  ANP K 502 "
        pdb=" O3A ANP K 502 "
        pdb=" PB  ANP K 502 "
      ideal   model   delta    sigma   weight residual
     125.41  115.37   10.04 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" CA  LYS K 430 "
        pdb=" CB  LYS K 430 "
        pdb=" CG  LYS K 430 "
      ideal   model   delta    sigma   weight residual
     114.10  120.59   -6.49 2.00e+00 2.50e-01 1.05e+01
  ... (remaining 13445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.79: 5758
       30.79 -    61.58: 250
       61.58 -    92.38: 31
       92.38 -   123.17: 2
      123.17 -   153.96: 11
  Dihedral angle restraints: 6052
    sinusoidal: 2525
      harmonic: 3527
  Sorted by residual:
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -139.51 -151.22     1      2.00e+01 2.50e-03 4.50e+01
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -37.09  141.68     1      2.00e+01 2.50e-03 4.28e+01
  dihedral pdb=" O5' GTP A 501 "
           pdb=" O3A GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" PB  GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   50.92 -136.80     1      2.00e+01 2.50e-03 4.15e+01
  ... (remaining 6049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1076
       0.043 -    0.086: 298
       0.086 -    0.128: 100
       0.128 -    0.171: 22
       0.171 -    0.214: 3
  Chirality restraints: 1499
  Sorted by residual:
  chirality pdb=" C2' ANP K 502 "
            pdb=" C1' ANP K 502 "
            pdb=" C3' ANP K 502 "
            pdb=" O2' ANP K 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.72   -2.51   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C3' ANP K 502 "
            pdb=" C2' ANP K 502 "
            pdb=" C4' ANP K 502 "
            pdb=" O3' ANP K 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.55    0.19 2.00e-01 2.50e+01 9.17e-01
  chirality pdb=" CB  THR K 400 "
            pdb=" CA  THR K 400 "
            pdb=" OG1 THR K 400 "
            pdb=" CG2 THR K 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 8.41e-01
  ... (remaining 1496 not shown)

  Planarity restraints: 1743
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  88 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO A  89 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP K 333 "   -0.009 2.00e-02 2.50e+03   1.74e-02 3.01e+00
        pdb=" C   ASP K 333 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ASP K 333 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU K 334 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA K 298 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.71e+00
        pdb=" C   ALA K 298 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   ALA K 298 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR K 299 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1740 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 85
        2.58 -     3.16: 7965
        3.16 -     3.74: 14551
        3.74 -     4.32: 20013
        4.32 -     4.90: 34302
  Nonbonded interactions: 76916
  Sorted by model distance:
  nonbonded pdb=" O1G GTP A 501 "
            pdb="MG    MG A 502 "
     model   vdw
     2.003 2.170
  nonbonded pdb=" OD1 ASN K 244 "
            pdb=" OG1 THR K 247 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" OE1 GLU A  71 "
            pdb="MG    MG A 502 "
     model   vdw
     2.122 2.170
  nonbonded pdb=" OG1 THR K 180 "
            pdb=" OG1 THR K 400 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" O   TYR K 235 "
            pdb=" OG1 THR K 238 "
     model   vdw
     2.144 3.040
  ... (remaining 76911 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=0.48 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:             2.100
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.100
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
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   0.116   9904  Z= 0.232
  Angle     :  0.790  15.092  13450  Z= 0.400
  Chirality :  0.046   0.214   1499
  Planarity :  0.005   0.053   1743
  Dihedral  : 18.721 153.961   3782
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 12.82 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: -0.36 (0.25), residues: 1209
  helix:  1.11 (0.24), residues: 495
  sheet: -1.34 (0.36), residues: 202
  loop : -1.06 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 221 
 TYR   0.022   0.001   TYR K 413 
 PHE   0.018   0.001   PHE K 182 
 TRP   0.012   0.001   TRP A  21 
 HIS   0.006   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 9904)
  covalent geometry    : angle       0.78979 (13450)
  hydrogen bonds       : bond        0.16271 (  443)
  hydrogen bonds       : angle       5.76108 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 196
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: K  193 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7292 (t-170)
REVERT: A  254 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7026 (mm-30)
REVERT: B   26 ASP cc_start: 0.8098 (t70) cc_final: 0.7863 (t0)
REVERT: B  328 GLU cc_start: 0.7560 (tt0) cc_final: 0.7234 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 198
  average time/residue: 0.1021
  time to fit residues: 28.2567
Evaluate side-chains
  189 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  187 THR
Chi-restraints excluded: chain K residue  193 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 133 GLN
B   8 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.139703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.102875 restraints weight = 22634.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.79
r_work: 0.3162 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   9904  Z= 0.266
  Angle     :  0.655   9.110  13450  Z= 0.326
  Chirality :  0.048   0.259   1499
  Planarity :  0.005   0.043   1743
  Dihedral  : 13.599 153.964   1494
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.78 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: -0.28 (0.25), residues: 1209
  helix:  0.98 (0.24), residues: 517
  sheet: -0.98 (0.34), residues: 212
  loop : -1.02 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 390 
 TYR   0.020   0.002   TYR A  24 
 PHE   0.018   0.002   PHE B 367 
 TRP   0.013   0.002   TRP B 344 
 HIS   0.011   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 ( 9904)
  covalent geometry    : angle       0.65478 (13450)
  hydrogen bonds       : bond        0.05250 (  443)
  hydrogen bonds       : angle       4.43836 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.369 
Fit side-chains
REVERT: K  421 LYS cc_start: 0.8525 (mttt) cc_final: 0.8291 (mttt)
REVERT: K  430 LYS cc_start: 0.8763 (mmmt) cc_final: 0.8545 (mmmt)
REVERT: A    1 MET cc_start: 0.5448 (mmm) cc_final: 0.5121 (mmm)
REVERT: A   24 TYR cc_start: 0.7778 (m-10) cc_final: 0.7570 (m-10)
REVERT: A  254 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7300 (mm-30)
REVERT: B   86 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8461 (ttm170)
REVERT: B  233 MET cc_start: 0.8452 (mtp) cc_final: 0.8187 (mtm)
REVERT: B  366 THR cc_start: 0.8453 (m) cc_final: 0.8241 (t)
  outliers start: 22
  outliers final: 15
  residues processed: 209
  average time/residue: 0.1014
  time to fit residues: 29.6683
Evaluate side-chains
  209 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 194
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  400 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 100 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
K 158 GLN
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 192 HIS
B 291 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.108638 restraints weight = 13010.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.07
r_work: 0.3284 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9904  Z= 0.120
  Angle     :  0.553   9.662  13450  Z= 0.271
  Chirality :  0.045   0.527   1499
  Planarity :  0.004   0.040   1743
  Dihedral  : 10.481 152.779   1491
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.34 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.08 (0.25), residues: 1209
  helix:  1.34 (0.24), residues: 516
  sheet: -0.66 (0.35), residues: 211
  loop : -0.98 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.011   0.001   PHE B 367 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9904)
  covalent geometry    : angle       0.55334 (13450)
  hydrogen bonds       : bond        0.03677 (  443)
  hydrogen bonds       : angle       4.06932 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.345 
Fit side-chains
REVERT: K  244 ASN cc_start: 0.8471 (t0) cc_final: 0.8132 (t0)
REVERT: K  421 LYS cc_start: 0.8470 (mttt) cc_final: 0.8217 (mttt)
REVERT: A    1 MET cc_start: 0.5645 (mmm) cc_final: 0.5360 (mmm)
REVERT: A   49 PHE cc_start: 0.6923 (m-80) cc_final: 0.6567 (m-80)
REVERT: A  254 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7171 (mm-30)
REVERT: A  279 GLU cc_start: 0.7997 (mp0) cc_final: 0.7741 (mp0)
REVERT: A  323 VAL cc_start: 0.8821 (t) cc_final: 0.8553 (m)
REVERT: B   26 ASP cc_start: 0.8441 (t0) cc_final: 0.8230 (t0)
REVERT: B   57 ASN cc_start: 0.8160 (m-40) cc_final: 0.7851 (t0)
REVERT: B  150 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7722 (tp)
REVERT: B  246 LEU cc_start: 0.8322 (tt) cc_final: 0.8077 (tp)
REVERT: B  322 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7570 (p)
REVERT: B  328 GLU cc_start: 0.7832 (tt0) cc_final: 0.7504 (tt0)
REVERT: B  366 THR cc_start: 0.8518 (m) cc_final: 0.8271 (t)
  outliers start: 17
  outliers final: 11
  residues processed: 211
  average time/residue: 0.1024
  time to fit residues: 30.2955
Evaluate side-chains
  210 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  283 LEU
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  322 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 100 optimal weight:    0.2980
   chunk 87 optimal weight:    0.0970
   chunk 68 optimal weight:    0.1980
   chunk 65 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0970
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.145559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.109876 restraints weight = 17572.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.48
r_work: 0.3283 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9904  Z= 0.093
  Angle     :  0.514   8.146  13450  Z= 0.251
  Chirality :  0.043   0.335   1499
  Planarity :  0.004   0.039   1743
  Dihedral  :  9.112 145.658   1491
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.10 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.45 (0.25), residues: 1209
  helix:  1.67 (0.24), residues: 517
  sheet: -0.39 (0.36), residues: 209
  loop : -0.85 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 221 
 TYR   0.010   0.001   TYR K 231 
 PHE   0.010   0.001   PHE A  52 
 TRP   0.014   0.001   TRP B 344 
 HIS   0.005   0.001   HIS K 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 9904)
  covalent geometry    : angle       0.51393 (13450)
  hydrogen bonds       : bond        0.03041 (  443)
  hydrogen bonds       : angle       3.86497 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 0.366 
Fit side-chains
REVERT: K  244 ASN cc_start: 0.8507 (t0) cc_final: 0.8167 (t0)
REVERT: K  333 ASP cc_start: 0.8058 (t0) cc_final: 0.7611 (t0)
REVERT: K  421 LYS cc_start: 0.8429 (mttt) cc_final: 0.8138 (mttt)
REVERT: A    1 MET cc_start: 0.5580 (mmm) cc_final: 0.5285 (mmm)
REVERT: A   62 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8580 (m)
REVERT: A  168 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: A  237 SER cc_start: 0.8776 (t) cc_final: 0.8537 (p)
REVERT: A  239 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (p)
REVERT: A  254 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7187 (mm-30)
REVERT: A  279 GLU cc_start: 0.8078 (mp0) cc_final: 0.7801 (mp0)
REVERT: A  362 VAL cc_start: 0.8721 (p) cc_final: 0.8520 (m)
REVERT: B   57 ASN cc_start: 0.8221 (m-40) cc_final: 0.7886 (t0)
REVERT: B  246 LEU cc_start: 0.8331 (tt) cc_final: 0.8110 (tp)
REVERT: B  322 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7591 (p)
  outliers start: 21
  outliers final: 10
  residues processed: 220
  average time/residue: 0.0961
  time to fit residues: 30.0112
Evaluate side-chains
  214 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 201
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  239 CYS
Chi-restraints excluded: chain B residue  322 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 119 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 95 optimal weight:    0.4980
   chunk 70 optimal weight:    0.2980
   chunk 75 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN
** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.143381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.107118 restraints weight = 21022.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.74
r_work: 0.3230 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9904  Z= 0.116
  Angle     :  0.522   8.172  13450  Z= 0.258
  Chirality :  0.043   0.290   1499
  Planarity :  0.004   0.043   1743
  Dihedral  :  9.021 145.888   1491
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.14 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.59 (0.25), residues: 1209
  helix:  1.78 (0.24), residues: 517
  sheet: -0.24 (0.36), residues: 207
  loop : -0.82 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 221 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.012   0.001   PHE A  52 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9904)
  covalent geometry    : angle       0.52180 (13450)
  hydrogen bonds       : bond        0.03397 (  443)
  hydrogen bonds       : angle       3.87780 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 203
  time to evaluate  : 0.352 
Fit side-chains
REVERT: K  113 MET cc_start: 0.5010 (mpp) cc_final: 0.4796 (mmp)
REVERT: K  244 ASN cc_start: 0.8480 (t0) cc_final: 0.8082 (t0)
REVERT: K  257 ASP cc_start: 0.7660 (p0) cc_final: 0.6632 (t0)
REVERT: K  421 LYS cc_start: 0.8425 (mttt) cc_final: 0.8136 (mttt)
REVERT: A    1 MET cc_start: 0.5523 (mmm) cc_final: 0.5213 (mmm)
REVERT: A   62 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8469 (m)
REVERT: A  237 SER cc_start: 0.8741 (t) cc_final: 0.8472 (p)
REVERT: A  239 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8390 (p)
REVERT: A  254 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7077 (mm-30)
REVERT: A  279 GLU cc_start: 0.7882 (mp0) cc_final: 0.7427 (mp0)
REVERT: B   57 ASN cc_start: 0.8134 (m-40) cc_final: 0.7820 (t0)
REVERT: B  150 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7664 (tp)
REVERT: B  246 LEU cc_start: 0.8285 (tt) cc_final: 0.8059 (tp)
REVERT: B  322 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7480 (p)
  outliers start: 18
  outliers final: 12
  residues processed: 211
  average time/residue: 0.0997
  time to fit residues: 29.7761
Evaluate side-chains
  213 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  322 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 2 optimal weight:   50.0000
   chunk 96 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0970
   chunk 57 optimal weight:    0.9980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  91 GLN
** A 216 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 = 0.3871 r_free = 0.3871 target = 0.142078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106196 restraints weight = 17986.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.51
r_work: 0.3221 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3054
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3054 r_free = 0.3054    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3054
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9904  Z= 0.143
  Angle     :  0.547   8.548  13450  Z= 0.271
  Chirality :  0.044   0.249   1499
  Planarity :  0.004   0.052   1743
  Dihedral  :  8.868 144.781   1491
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.76 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.58 (0.25), residues: 1209
  helix:  1.79 (0.24), residues: 516
  sheet: -0.29 (0.36), residues: 210
  loop : -0.82 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.017   0.001   TYR A  24 
 PHE   0.012   0.001   PHE B 367 
 TRP   0.012   0.001   TRP B 344 
 HIS   0.007   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 9904)
  covalent geometry    : angle       0.54698 (13450)
  hydrogen bonds       : bond        0.03746 (  443)
  hydrogen bonds       : angle       3.95116 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.290 
Fit side-chains
REVERT: K  113 MET cc_start: 0.4991 (mpp) cc_final: 0.4699 (mmp)
REVERT: K  167 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6637 (mm-40)
REVERT: K  244 ASN cc_start: 0.8566 (t0) cc_final: 0.8134 (t0)
REVERT: K  257 ASP cc_start: 0.7840 (p0) cc_final: 0.6875 (t70)
REVERT: K  260 ASN cc_start: 0.7727 (t0) cc_final: 0.7490 (t0)
REVERT: K  394 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8372 (mm)
REVERT: K  421 LYS cc_start: 0.8399 (mttt) cc_final: 0.8105 (mttt)
REVERT: A  254 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7434 (mm-30)
REVERT: A  279 GLU cc_start: 0.8129 (mp0) cc_final: 0.7664 (mp0)
REVERT: A  362 VAL cc_start: 0.8691 (m) cc_final: 0.8451 (p)
REVERT: B   57 ASN cc_start: 0.8280 (m-40) cc_final: 0.7877 (t0)
REVERT: B  150 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7883 (tp)
REVERT: B  246 LEU cc_start: 0.8408 (tt) cc_final: 0.8180 (tp)
REVERT: B  322 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7704 (p)
REVERT: B  328 GLU cc_start: 0.8007 (tt0) cc_final: 0.7686 (tt0)
REVERT: B  366 THR cc_start: 0.8480 (m) cc_final: 0.8217 (t)
REVERT: B  415 MET cc_start: 0.8294 (tpp) cc_final: 0.8080 (ttm)
  outliers start: 27
  outliers final: 19
  residues processed: 218
  average time/residue: 0.0932
  time to fit residues: 29.2530
Evaluate side-chains
  226 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 203
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  167 GLN
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  283 LEU
Chi-restraints excluded: chain K residue  394 LEU
Chi-restraints excluded: chain K residue  400 THR
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 105 optimal weight:    0.0970
   chunk 83 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 7 optimal weight:    7.9990
   chunk 69 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.144031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107499 restraints weight = 22469.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.85
r_work: 0.3231 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9904  Z= 0.101
  Angle     :  0.526   9.704  13450  Z= 0.259
  Chirality :  0.043   0.235   1499
  Planarity :  0.004   0.036   1743
  Dihedral  :  8.521 135.647   1491
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.33 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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 (0.25), residues: 1209
  helix:  1.76 (0.24), residues: 522
  sheet: -0.20 (0.36), residues: 207
  loop : -0.80 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.017   0.001   TYR A  24 
 PHE   0.010   0.001   PHE B 367 
 TRP   0.013   0.001   TRP B 344 
 HIS   0.006   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9904)
  covalent geometry    : angle       0.52571 (13450)
  hydrogen bonds       : bond        0.03178 (  443)
  hydrogen bonds       : angle       3.89812 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 202
  time to evaluate  : 0.446 
Fit side-chains
REVERT: K  113 MET cc_start: 0.5065 (mpp) cc_final: 0.4795 (mmp)
REVERT: K  236 ASN cc_start: 0.8697 (m-40) cc_final: 0.8302 (m-40)
REVERT: K  244 ASN cc_start: 0.8529 (t0) cc_final: 0.8076 (t0)
REVERT: K  257 ASP cc_start: 0.7704 (p0) cc_final: 0.6687 (t70)
REVERT: K  421 LYS cc_start: 0.8376 (mttt) cc_final: 0.8090 (mttt)
REVERT: A    3 GLU cc_start: 0.7620 (mp0) cc_final: 0.7001 (pm20)
REVERT: A  210 TYR cc_start: 0.8414 (m-10) cc_final: 0.7369 (m-10)
REVERT: A  237 SER cc_start: 0.8704 (t) cc_final: 0.8462 (p)
REVERT: A  254 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7230 (mm-30)
REVERT: A  279 GLU cc_start: 0.7911 (mp0) cc_final: 0.7606 (mp0)
REVERT: A  362 VAL cc_start: 0.8624 (m) cc_final: 0.8418 (p)
REVERT: A  425 MET cc_start: 0.8046 (mmm) cc_final: 0.7773 (tpp)
REVERT: B   57 ASN cc_start: 0.8124 (m-40) cc_final: 0.7785 (t0)
REVERT: B  150 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7661 (tp)
REVERT: B  322 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7462 (p)
REVERT: B  328 GLU cc_start: 0.7813 (tt0) cc_final: 0.7502 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 215
  average time/residue: 0.0942
  time to fit residues: 29.0725
Evaluate side-chains
  218 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 199
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  283 LEU
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
K 260 ASN
** K 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  15 GLN
A 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.140219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.104293 restraints weight = 18077.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.49
r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9904  Z= 0.202
  Angle     :  0.596   9.974  13450  Z= 0.295
  Chirality :  0.045   0.245   1499
  Planarity :  0.004   0.040   1743
  Dihedral  :  8.136 138.208   1491
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.05 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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 (0.25), residues: 1209
  helix:  1.68 (0.24), residues: 514
  sheet: -0.10 (0.36), residues: 200
  loop : -0.89 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.021   0.001   TYR A  24 
 PHE   0.015   0.002   PHE A 141 
 TRP   0.009   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 9904)
  covalent geometry    : angle       0.59566 (13450)
  hydrogen bonds       : bond        0.04362 (  443)
  hydrogen bonds       : angle       4.12216 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 210
  time to evaluate  : 0.378 
Fit side-chains
REVERT: K  113 MET cc_start: 0.4944 (mpp) cc_final: 0.4650 (mmp)
REVERT: K  167 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6728 (mm-40)
REVERT: K  244 ASN cc_start: 0.8615 (t0) cc_final: 0.8140 (t0)
REVERT: K  279 MET cc_start: 0.6403 (mmm) cc_final: 0.6093 (mmm)
REVERT: K  421 LYS cc_start: 0.8397 (mttt) cc_final: 0.8082 (mttt)
REVERT: A  254 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7462 (mm-30)
REVERT: A  275 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8025 (m)
REVERT: A  279 GLU cc_start: 0.8183 (mp0) cc_final: 0.7745 (mp0)
REVERT: A  362 VAL cc_start: 0.8720 (m) cc_final: 0.8474 (p)
REVERT: A  390 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7934 (mtm180)
REVERT: B   57 ASN cc_start: 0.8288 (m-40) cc_final: 0.7967 (t0)
REVERT: B  150 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7986 (tp)
REVERT: B  212 PHE cc_start: 0.7969 (t80) cc_final: 0.7668 (t80)
REVERT: B  328 GLU cc_start: 0.8097 (tt0) cc_final: 0.7784 (tt0)
REVERT: B  366 THR cc_start: 0.8478 (m) cc_final: 0.8233 (t)
  outliers start: 28
  outliers final: 23
  residues processed: 225
  average time/residue: 0.0947
  time to fit residues: 30.3942
Evaluate side-chains
  235 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 209
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  167 GLN
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  260 ASN
Chi-restraints excluded: chain K residue  329 LEU
Chi-restraints excluded: chain K residue  400 THR
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 25 optimal weight:   20.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
K 260 ASN
** K 355 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 = 0.3854 r_free = 0.3854 target = 0.140688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.105433 restraints weight = 15206.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.25
r_work: 0.3218 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9904  Z= 0.177
  Angle     :  0.591  10.683  13450  Z= 0.292
  Chirality :  0.045   0.233   1499
  Planarity :  0.004   0.041   1743
  Dihedral  :  7.884 138.930   1491
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.43 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.45 (0.25), residues: 1209
  helix:  1.63 (0.24), residues: 513
  sheet: -0.05 (0.36), residues: 199
  loop : -0.95 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.019   0.001   TYR A  24 
 PHE   0.011   0.001   PHE A 141 
 TRP   0.010   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9904)
  covalent geometry    : angle       0.59050 (13450)
  hydrogen bonds       : bond        0.04063 (  443)
  hydrogen bonds       : angle       4.12293 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 0.369 
Fit side-chains
REVERT: K  113 MET cc_start: 0.4926 (mpp) cc_final: 0.4638 (mmp)
REVERT: K  167 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6756 (mm-40)
REVERT: K  244 ASN cc_start: 0.8611 (t0) cc_final: 0.8144 (t0)
REVERT: K  279 MET cc_start: 0.6433 (mmm) cc_final: 0.6098 (mmm)
REVERT: K  421 LYS cc_start: 0.8356 (mttt) cc_final: 0.8059 (mttt)
REVERT: A    3 GLU cc_start: 0.7795 (mp0) cc_final: 0.7194 (pm20)
REVERT: A  218 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (t0)
REVERT: A  254 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7406 (mm-30)
REVERT: A  275 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (m)
REVERT: A  279 GLU cc_start: 0.8109 (mp0) cc_final: 0.7640 (mp0)
REVERT: A  362 VAL cc_start: 0.8706 (m) cc_final: 0.8456 (p)
REVERT: A  390 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7901 (mtm180)
REVERT: B   57 ASN cc_start: 0.8277 (m-40) cc_final: 0.7878 (t0)
REVERT: B  150 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7894 (tp)
REVERT: B  212 PHE cc_start: 0.7930 (t80) cc_final: 0.7631 (t80)
REVERT: B  328 GLU cc_start: 0.8025 (tt0) cc_final: 0.7713 (tt0)
REVERT: B  366 THR cc_start: 0.8470 (m) cc_final: 0.8222 (t)
REVERT: B  415 MET cc_start: 0.8308 (tpp) cc_final: 0.8056 (ttm)
  outliers start: 29
  outliers final: 23
  residues processed: 227
  average time/residue: 0.0927
  time to fit residues: 30.1522
Evaluate side-chains
  233 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 206
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  106 ILE
Chi-restraints excluded: chain K residue  167 GLN
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  400 THR
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 25 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 52 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
K 260 ASN
** K 355 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 = 0.3854 r_free = 0.3854 target = 0.140629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.105529 restraints weight = 15242.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.23
r_work: 0.3225 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9904  Z= 0.176
  Angle     :  0.589  11.017  13450  Z= 0.293
  Chirality :  0.045   0.230   1499
  Planarity :  0.004   0.040   1743
  Dihedral  :  7.770 138.217   1491
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.52 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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: 1209
  helix:  1.60 (0.24), residues: 514
  sheet: -0.05 (0.36), residues: 199
  loop : -1.00 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.021   0.001   TYR A  24 
 PHE   0.012   0.001   PHE A 141 
 TRP   0.010   0.002   TRP B 344 
 HIS   0.007   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 9904)
  covalent geometry    : angle       0.58865 (13450)
  hydrogen bonds       : bond        0.04094 (  443)
  hydrogen bonds       : angle       4.15681 ( 1253)

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

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

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2418 Ramachandran restraints generated.
    1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 0.384 
Fit side-chains
REVERT: K  113 MET cc_start: 0.4921 (mpp) cc_final: 0.4718 (mmp)
REVERT: K  167 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6751 (mm-40)
REVERT: K  244 ASN cc_start: 0.8585 (t0) cc_final: 0.8110 (t0)
REVERT: K  421 LYS cc_start: 0.8356 (mttt) cc_final: 0.8055 (mttt)
REVERT: K  430 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8309 (mmmt)
REVERT: A    3 GLU cc_start: 0.7801 (mp0) cc_final: 0.7187 (pm20)
REVERT: A  218 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7914 (t0)
REVERT: A  254 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7385 (mm-30)
REVERT: A  275 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7991 (m)
REVERT: A  279 GLU cc_start: 0.8118 (mp0) cc_final: 0.7646 (mp0)
REVERT: A  362 VAL cc_start: 0.8703 (m) cc_final: 0.8458 (p)
REVERT: A  390 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7907 (mtm180)
REVERT: B   57 ASN cc_start: 0.8268 (m-40) cc_final: 0.7869 (t0)
REVERT: B  150 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7870 (tp)
REVERT: B  212 PHE cc_start: 0.7917 (t80) cc_final: 0.6850 (m-80)
REVERT: B  328 GLU cc_start: 0.8001 (tt0) cc_final: 0.7687 (tt0)
REVERT: B  366 THR cc_start: 0.8470 (m) cc_final: 0.8213 (t)
REVERT: B  415 MET cc_start: 0.8301 (tpp) cc_final: 0.8054 (ttm)
  outliers start: 30
  outliers final: 25
  residues processed: 227
  average time/residue: 0.0951
  time to fit residues: 30.5990
Evaluate side-chains
  237 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  106 ILE
Chi-restraints excluded: chain K residue  167 GLN
Chi-restraints excluded: chain K residue  259 ASN
Chi-restraints excluded: chain K residue  260 ASN
Chi-restraints excluded: chain K residue  400 THR
Chi-restraints excluded: chain K residue  404 VAL
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue  163 LYS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  295 CYS
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  432 TYR
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   31 ASP
Chi-restraints excluded: chain B residue   39 ASP
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  147 MET
Chi-restraints excluded: chain B residue  150 LEU
Chi-restraints excluded: chain B residue  163 ILE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  316 ILE
Chi-restraints excluded: chain B residue  322 SER
Chi-restraints excluded: chain B residue  381 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 90 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
K 259 ASN
K 260 ASN
** K 355 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 = 0.3854 r_free = 0.3854 target = 0.140576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.105238 restraints weight = 15700.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.25
r_work: 0.3221 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3063 r_free = 0.3063    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9904  Z= 0.180
  Angle     :  0.597  10.999  13450  Z= 0.298
  Chirality :  0.045   0.229   1499
  Planarity :  0.004   0.043   1743
  Dihedral  :  7.727 137.956   1491
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.24 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.00 %
    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:  0.39 (0.25), residues: 1209
  helix:  1.59 (0.24), residues: 514
  sheet: -0.12 (0.35), residues: 210
  loop : -1.00 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 359 
 TYR   0.019   0.001   TYR A  24 
 PHE   0.012   0.002   PHE A 141 
 TRP   0.010   0.002   TRP B 344 
 HIS   0.008   0.001   HIS B  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9904)
  covalent geometry    : angle       0.59697 (13450)
  hydrogen bonds       : bond        0.04124 (  443)
  hydrogen bonds       : angle       4.17117 ( 1253)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2963.21 seconds
wall clock time: 51 minutes 26.24 seconds (3086.24 seconds total)