Starting phenix.real_space_refine
on Sat Apr  4 23:41:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6z3z_11067/04_2026/6z3z_11067.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4121      2.51       5
     N     931      2.21       5
     O    1019      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6115
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3061
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 10, 'TRANS': 374}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 3054
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 9, 'TRANS': 374}
          Chain breaks: 5
  Time building chain proxies: 1.52, per 1000 atoms: 0.25
  Number of scatterers: 6115
  At special positions: 0
  Unit cell: (77.8125, 87.15, 102.713, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1019      8.00
     N     931      7.00
     C    4121      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: 0.45
  Conformation dependent library (CDL) restraints added in 386.1 milliseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      82.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 25 through 44
      removed outlier: 3.629A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LEU B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 59
      removed outlier: 3.596A  pdb=" N   VAL B  57 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 66
      removed outlier: 3.862A  pdb=" N   LEU B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ILE B  65 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  66 " --> pdb=" O   MET B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 60 through 66'
    Processing helix  chain 'B' and resid 125 through 129
    Processing helix  chain 'B' and resid 131 through 136
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 3.674A  pdb=" N   HIS B 145 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 165
    Processing helix  chain 'B' and resid 165 through 188
      removed outlier: 4.086A  pdb=" N   GLY B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   THR B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLY B 178 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU B 179 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   TYR B 182 " --> pdb=" O   GLY B 178 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   PHE B 184 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 185 " --> pdb=" O   MET B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 211
    Processing helix  chain 'B' and resid 216 through 227
    Processing helix  chain 'B' and resid 229 through 256
      removed outlier: 4.317A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ALA B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 249 " --> pdb=" O   ALA B 245 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 252 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 303
      removed outlier: 3.622A  pdb=" N   ALA B 293 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.760A  pdb=" N   PHE B 324 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA B 327 " --> pdb=" O   ALA B 323 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 341
      removed outlier: 3.571A  pdb=" N   LEU B 339 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 353
      removed outlier: 3.589A  pdb=" N   ALA B 346 " --> pdb=" O   GLY B 342 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   TYR B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 4.901A  pdb=" N   ASN B 351 " --> pdb=" O   HIS B 347 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   LEU B 353 " --> pdb=" O   THR B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 371
      removed outlier: 4.270A  pdb=" N   ARG B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS B 362 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 385
      removed outlier: 4.085A  pdb=" N   VAL B 375 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   MET B 380 " --> pdb=" O   ILE B 376 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA B 383 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 384 " --> pdb=" O   MET B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 410
      removed outlier: 3.992A  pdb=" N   PHE B 405 " --> pdb=" O   PHE B 401 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ARG B 408 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 422
      removed outlier: 3.827A  pdb=" N   GLY B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 431
      removed outlier: 3.843A  pdb=" N   PHE B 431 " --> pdb=" O   PRO B 428 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 428 through 431'
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 4.246A  pdb=" N   MET B 436 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   SER B 438 " --> pdb=" O   MET B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.837A  pdb=" N   LEU B 448 " --> pdb=" O   ILE B 444 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA B 449 " --> pdb=" O   ALA B 445 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE B 450 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 444 through 450'
    Processing helix  chain 'B' and resid 458 through 474
      removed outlier: 3.965A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TRP B 474 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
      removed outlier: 3.567A  pdb=" N   GLY B 478 " --> pdb=" O   TRP B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 488
    Processing helix  chain 'A' and resid 25 through 44
      removed outlier: 3.504A  pdb=" N   PHE A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A  33 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A  38 " --> pdb=" O   THR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 68
      removed outlier: 4.449A  pdb=" N   GLY A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU A  60 " --> pdb=" O   MET A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
      removed outlier: 3.555A  pdb=" N   THR A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 124 through 128'
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.792A  pdb=" N   ASN A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.537A  pdb=" N   ILE A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   HIS A 145 " --> pdb=" O   PRO A 141 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 146 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 165
      removed outlier: 3.611A  pdb=" N   TYR A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 188
      removed outlier: 3.515A  pdb=" N   ILE A 175 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLY A 178 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 212
      removed outlier: 3.693A  pdb=" N   PHE A 206 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 229 through 257
      removed outlier: 3.806A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL A 241 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   TYR A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   SER A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 303
      removed outlier: 3.930A  pdb=" N   SER A 274 " --> pdb=" O   ALA A 270 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA A 293 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 330
      removed outlier: 3.891A  pdb=" N   THR A 313 " --> pdb=" O   PRO A 309 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   GLY A 314 " --> pdb=" O   MET A 310 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 341
    Processing helix  chain 'A' and resid 343 through 348
      removed outlier: 3.764A  pdb=" N   HIS A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 4.543A  pdb=" N   ARG A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 385
      removed outlier: 4.137A  pdb=" N   TYR A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   MET A 380 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 385 " --> pdb=" O   GLY A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.766A  pdb=" N   ILE A 391 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 408
      removed outlier: 3.629A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   PHE A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 406 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG A 408 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 420
    Processing helix  chain 'A' and resid 432 through 437
      removed outlier: 3.830A  pdb=" N   MET A 436 " --> pdb=" O   GLN A 432 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 437 " --> pdb=" O   HIS A 433 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 432 through 437'
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 4.193A  pdb=" N   LEU A 448 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A 449 " --> pdb=" O   ALA A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.593A  pdb=" N   LEU A 468 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 475 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   PHE A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 488
      removed outlier: 4.182A  pdb=" N   GLU A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1026 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: 0.87

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1758
        1.34 -     1.46: 1130
        1.46 -     1.57: 3318
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 6282
  Sorted by residual:
  bond pdb=" N   ARG A 408 "
       pdb=" CA  ARG A 408 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.32e-02 5.74e+03 7.60e+00
  bond pdb=" N   ARG B 441 "
       pdb=" CA  ARG B 441 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.19e-02 7.06e+03 7.32e+00
  bond pdb=" N   PHE B 129 "
       pdb=" CA  PHE B 129 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.92e+00
  bond pdb=" N   THR B 128 "
       pdb=" CA  THR B 128 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.030 1.32e-02 5.74e+03 5.13e+00
  bond pdb=" N   ASP B 130 "
       pdb=" CA  ASP B 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.41e-02 5.03e+03 5.09e+00
  ... (remaining 6277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 8274
        1.68 -     3.36: 180
        3.36 -     5.04: 41
        5.04 -     6.73: 7
        6.73 -     8.41: 4
  Bond angle restraints: 8506
  Sorted by residual:
  angle pdb=" N   MET B 127 "
        pdb=" CA  MET B 127 "
        pdb=" C   MET B 127 "
      ideal   model   delta    sigma   weight residual
     112.87  108.14    4.73 1.20e+00 6.94e-01 1.56e+01
  angle pdb=" C   VAL B 228 "
        pdb=" N   ASP B 229 "
        pdb=" CA  ASP B 229 "
      ideal   model   delta    sigma   weight residual
     121.80  129.62   -7.82 2.44e+00 1.68e-01 1.03e+01
  angle pdb=" CA  GLU B 132 "
        pdb=" C   GLU B 132 "
        pdb=" O   GLU B 132 "
      ideal   model   delta    sigma   weight residual
     120.90  117.52    3.38 1.07e+00 8.73e-01 9.97e+00
  angle pdb=" CA  ARG B 441 "
        pdb=" C   ARG B 441 "
        pdb=" O   ARG B 441 "
      ideal   model   delta    sigma   weight residual
     120.65  116.93    3.72 1.23e+00 6.61e-01 9.17e+00
  angle pdb=" CB  ARG B 441 "
        pdb=" CG  ARG B 441 "
        pdb=" CD  ARG B 441 "
      ideal   model   delta    sigma   weight residual
     111.30  117.76   -6.46 2.30e+00 1.89e-01 7.88e+00
  ... (remaining 8501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3206
       17.91 -    35.81: 285
       35.81 -    53.72: 43
       53.72 -    71.63: 4
       71.63 -    89.53: 6
  Dihedral angle restraints: 3544
    sinusoidal: 1329
      harmonic: 2215
  Sorted by residual:
  dihedral pdb=" CA  ASP B 452 "
           pdb=" C   ASP B 452 "
           pdb=" N   THR B 453 "
           pdb=" CA  THR B 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.61   22.39     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CB  GLU B 483 "
           pdb=" CG  GLU B 483 "
           pdb=" CD  GLU B 483 "
           pdb=" OE1 GLU B 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.53   89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU B 239 "
           pdb=" CG  GLU B 239 "
           pdb=" CD  GLU B 239 "
           pdb=" OE1 GLU B 239 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.34   87.34     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 3541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 597
       0.030 -    0.059: 292
       0.059 -    0.089: 63
       0.089 -    0.119: 23
       0.119 -    0.148: 6
  Chirality restraints: 981
  Sorted by residual:
  chirality pdb=" CA  MET B 127 "
            pdb=" N   MET B 127 "
            pdb=" C   MET B 127 "
            pdb=" CB  MET B 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  PRO B 131 "
            pdb=" N   PRO B 131 "
            pdb=" C   PRO B 131 "
            pdb=" CB  PRO B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.87   -0.15 2.00e-01 2.50e+01 5.39e-01
  chirality pdb=" CB  ILE A 450 "
            pdb=" CA  ILE A 450 "
            pdb=" CG1 ILE A 450 "
            pdb=" CG2 ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 978 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 308 "    0.039 5.00e-02 4.00e+02   5.94e-02 5.64e+00
        pdb=" N   PRO A 309 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 309 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 309 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 139 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.76e+00
        pdb=" N   PRO B 140 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 140 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 140 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 413 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO A 414 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 414 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 414 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 356
        2.74 -     3.28: 6872
        3.28 -     3.82: 9676
        3.82 -     4.36: 11671
        4.36 -     4.90: 18847
  Nonbonded interactions: 47422
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 382 "
            pdb=" OG1 THR A 386 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" N   GLU B 132 "
            pdb=" OE1 GLU B 132 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   LYS A  42 "
            pdb=" NH1 ARG A  45 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   LEU A 299 "
            pdb=" OG1 THR A 303 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG  SER A 455 "
            pdb=" OE1 GLN A 459 "
     model   vdw
     2.283 3.040
  ... (remaining 47417 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 23 through 258 or resid 269 through 488))
}

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=1.00 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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.520
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
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      :  0.003   0.051   6282  Z= 0.152
  Angle     :  0.621   8.408   8506  Z= 0.326
  Chirality :  0.037   0.148    981
  Planarity :  0.004   0.059   1032
  Dihedral  : 13.781  89.534   2114
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.62 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.32), residues: 745
  helix:  0.30 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.12 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  45 
 TYR   0.011   0.001   TYR B 350 
 PHE   0.015   0.001   PHE B 377 
 TRP   0.009   0.001   TRP A 429 
 HIS   0.003   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6282)
  covalent geometry    : angle       0.62116 ( 8506)
  hydrogen bonds       : bond        0.28921 (  346)
  hydrogen bonds       : angle       7.71655 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 179
  time to evaluate  : 0.161 
Fit side-chains
REVERT: B  398 LEU cc_start: 0.7378 (pt) cc_final: 0.6945 (tp)
REVERT: A   29 PHE cc_start: 0.5911 (m-10) cc_final: 0.5142 (m-10)
REVERT: A   41 PHE cc_start: 0.6853 (m-80) cc_final: 0.6631 (m-10)
REVERT: A  440 LEU cc_start: 0.7342 (mm) cc_final: 0.6990 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0557
  time to fit residues: 14.3142
Evaluate side-chains
  136 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 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:
A 157 GLN
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.114828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.104089 restraints weight = 18735.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 4.08
r_work: 0.3665 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6282  Z= 0.227
  Angle     :  0.772  10.226   8506  Z= 0.395
  Chirality :  0.045   0.153    981
  Planarity :  0.005   0.054   1032
  Dihedral  :  4.701  19.349    801
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.64 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.31), residues: 745
  helix:  0.35 (0.22), residues: 564
  sheet:  None (None), residues: 0
  loop : -1.92 (0.49), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  45 
 TYR   0.016   0.002   TYR A 379 
 PHE   0.049   0.002   PHE A 470 
 TRP   0.016   0.002   TRP B 474 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 6282)
  covalent geometry    : angle       0.77184 ( 8506)
  hydrogen bonds       : bond        0.05228 (  346)
  hydrogen bonds       : angle       5.26089 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  126 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8425 (tttt)
REVERT: B  359 MET cc_start: 0.7733 (ptt) cc_final: 0.7490 (ptt)
REVERT: B  376 ILE cc_start: 0.7453 (mm) cc_final: 0.6613 (mt)
REVERT: A  184 PHE cc_start: 0.8172 (p90) cc_final: 0.7822 (p90)
REVERT: A  188 MET cc_start: 0.7822 (mmp) cc_final: 0.7161 (mmt)
REVERT: A  440 LEU cc_start: 0.7890 (mm) cc_final: 0.7615 (mm)
  outliers start: 6
  outliers final: 4
  residues processed: 159
  average time/residue: 0.0544
  time to fit residues: 12.6508
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  429 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 51 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 273 GLN
B 277 ASN
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 411 ASN
A 433 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.119027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.108347 restraints weight = 18186.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 4.12
r_work: 0.3739 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6282  Z= 0.134
  Angle     :  0.678   9.093   8506  Z= 0.339
  Chirality :  0.040   0.141    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.428  17.817    801
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.33 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.32), residues: 745
  helix:  0.50 (0.22), residues: 567
  sheet:  None (None), residues: 0
  loop : -1.71 (0.51), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  45 
 TYR   0.012   0.001   TYR A 379 
 PHE   0.046   0.001   PHE A 470 
 TRP   0.009   0.001   TRP B 429 
 HIS   0.004   0.001   HIS A 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6282)
  covalent geometry    : angle       0.67765 ( 8506)
  hydrogen bonds       : bond        0.04189 (  346)
  hydrogen bonds       : angle       4.78746 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8690 (pp)
REVERT: B  376 ILE cc_start: 0.7321 (mm) cc_final: 0.6227 (mt)
REVERT: B  434 MET cc_start: 0.7891 (mpp) cc_final: 0.7295 (mtm)
REVERT: B  454 GLU cc_start: 0.8216 (tp30) cc_final: 0.8007 (tp30)
REVERT: A  184 PHE cc_start: 0.8146 (p90) cc_final: 0.7870 (p90)
REVERT: A  321 TRP cc_start: 0.8746 (t60) cc_final: 0.8517 (t60)
REVERT: A  344 THR cc_start: 0.7621 (p) cc_final: 0.7418 (p)
REVERT: A  359 MET cc_start: 0.7904 (ppp) cc_final: 0.7213 (ppp)
REVERT: A  363 GLN cc_start: 0.7928 (mt0) cc_final: 0.7335 (mt0)
REVERT: A  440 LEU cc_start: 0.7676 (mm) cc_final: 0.7386 (mm)
  outliers start: 12
  outliers final: 5
  residues processed: 159
  average time/residue: 0.0538
  time to fit residues: 12.5779
Evaluate side-chains
  145 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  244 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.118972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.108202 restraints weight = 18209.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3869 rms_B_bonded: 4.13
r_work: 0.3744 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6282  Z= 0.132
  Angle     :  0.672   9.872   8506  Z= 0.332
  Chirality :  0.040   0.137    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.354  17.239    801
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 20.49 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.32), residues: 745
  helix:  0.58 (0.22), residues: 565
  sheet:  None (None), residues: 0
  loop : -1.50 (0.52), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.011   0.001   TYR A 379 
 PHE   0.041   0.001   PHE A 470 
 TRP   0.009   0.001   TRP B 429 
 HIS   0.003   0.001   HIS A 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6282)
  covalent geometry    : angle       0.67202 ( 8506)
  hydrogen bonds       : bond        0.03864 (  346)
  hydrogen bonds       : angle       4.61383 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: B  376 ILE cc_start: 0.7051 (mm) cc_final: 0.6200 (mm)
REVERT: B  434 MET cc_start: 0.7911 (mpp) cc_final: 0.7385 (mtm)
REVERT: B  454 GLU cc_start: 0.8072 (tp30) cc_final: 0.7821 (tp30)
REVERT: A  184 PHE cc_start: 0.8060 (p90) cc_final: 0.7648 (p90)
REVERT: A  188 MET cc_start: 0.7896 (mmp) cc_final: 0.7164 (mmt)
REVERT: A  321 TRP cc_start: 0.8761 (t60) cc_final: 0.8294 (t60)
REVERT: A  359 MET cc_start: 0.7751 (ppp) cc_final: 0.7190 (ppp)
REVERT: A  363 GLN cc_start: 0.7889 (mt0) cc_final: 0.7384 (mt0)
REVERT: A  440 LEU cc_start: 0.7661 (mm) cc_final: 0.7411 (mm)
  outliers start: 12
  outliers final: 6
  residues processed: 155
  average time/residue: 0.0514
  time to fit residues: 11.9254
Evaluate side-chains
  152 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 146
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  461 MET
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  133 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 71 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.119124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.108124 restraints weight = 18818.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 4.21
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6282  Z= 0.135
  Angle     :  0.674  10.550   8506  Z= 0.335
  Chirality :  0.040   0.120    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.364  16.752    801
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.88 %
    Favored  : 75.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.32), residues: 745
  helix:  0.58 (0.22), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.29 (0.54), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.017   0.001   TYR A 379 
 PHE   0.038   0.001   PHE A 470 
 TRP   0.008   0.001   TRP B 474 
 HIS   0.002   0.001   HIS A 433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6282)
  covalent geometry    : angle       0.67372 ( 8506)
  hydrogen bonds       : bond        0.03754 (  346)
  hydrogen bonds       : angle       4.53455 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.221 
Fit side-chains
REVERT: B   25 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8752 (pp)
REVERT: B  376 ILE cc_start: 0.6332 (mm) cc_final: 0.6107 (mm)
REVERT: B  454 GLU cc_start: 0.8107 (tp30) cc_final: 0.7862 (tp30)
REVERT: A  359 MET cc_start: 0.7777 (ppp) cc_final: 0.7118 (ppp)
REVERT: A  363 GLN cc_start: 0.7754 (mt0) cc_final: 0.7137 (mt0)
REVERT: A  434 MET cc_start: 0.7044 (tpt) cc_final: 0.6560 (mmm)
REVERT: A  440 LEU cc_start: 0.7633 (mm) cc_final: 0.7400 (mm)
  outliers start: 20
  outliers final: 9
  residues processed: 162
  average time/residue: 0.0523
  time to fit residues: 12.6747
Evaluate side-chains
  154 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain B residue  461 MET
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  290 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 71 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.119701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.108870 restraints weight = 18424.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 4.16
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6282  Z= 0.132
  Angle     :  0.683   7.770   8506  Z= 0.338
  Chirality :  0.040   0.123    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.357  17.162    801
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 24.81 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.32), residues: 745
  helix:  0.57 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.42 (0.52), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 441 
 TYR   0.012   0.001   TYR A 379 
 PHE   0.040   0.001   PHE A 470 
 TRP   0.008   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6282)
  covalent geometry    : angle       0.68343 ( 8506)
  hydrogen bonds       : bond        0.03614 (  346)
  hydrogen bonds       : angle       4.43301 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8759 (pp)
REVERT: B  376 ILE cc_start: 0.6535 (mm) cc_final: 0.6119 (mm)
REVERT: A  359 MET cc_start: 0.7705 (ppp) cc_final: 0.7058 (ppp)
REVERT: A  363 GLN cc_start: 0.7804 (mt0) cc_final: 0.7215 (mt0)
REVERT: A  437 PHE cc_start: 0.7591 (m-80) cc_final: 0.7374 (m-80)
REVERT: A  440 LEU cc_start: 0.7682 (mm) cc_final: 0.7418 (mm)
REVERT: A  458 LYS cc_start: 0.7455 (tttt) cc_final: 0.7117 (tptt)
  outliers start: 21
  outliers final: 11
  residues processed: 167
  average time/residue: 0.0557
  time to fit residues: 13.6958
Evaluate side-chains
  161 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 149
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  288 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0370
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0670
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.2372

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.122398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.111629 restraints weight = 18450.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 4.29
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6282  Z= 0.132
  Angle     :  0.714  10.221   8506  Z= 0.350
  Chirality :  0.040   0.155    981
  Planarity :  0.004   0.060   1032
  Dihedral  :  4.288  17.049    801
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.04 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 571
  sheet:  None (None), residues: 0
  loop : -1.45 (0.53), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.008   0.001   TYR A 182 
 PHE   0.041   0.001   PHE A 470 
 TRP   0.010   0.001   TRP B 321 
 HIS   0.003   0.001   HIS B 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6282)
  covalent geometry    : angle       0.71392 ( 8506)
  hydrogen bonds       : bond        0.03529 (  346)
  hydrogen bonds       : angle       4.38592 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.222 
Fit side-chains
REVERT: B  239 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: B  376 ILE cc_start: 0.6460 (mm) cc_final: 0.6054 (mm)
REVERT: B  380 MET cc_start: 0.5852 (ptt) cc_final: 0.5612 (ttp)
REVERT: B  437 PHE cc_start: 0.7992 (m-80) cc_final: 0.7775 (m-80)
REVERT: A  321 TRP cc_start: 0.8577 (t60) cc_final: 0.8142 (t60)
REVERT: A  328 GLU cc_start: 0.7715 (tp30) cc_final: 0.7096 (tt0)
REVERT: A  359 MET cc_start: 0.7670 (ppp) cc_final: 0.7056 (ppp)
REVERT: A  363 GLN cc_start: 0.7749 (mt0) cc_final: 0.7188 (mt0)
REVERT: A  434 MET cc_start: 0.6420 (tpt) cc_final: 0.6169 (mmm)
REVERT: A  440 LEU cc_start: 0.7604 (mm) cc_final: 0.7350 (mm)
  outliers start: 18
  outliers final: 9
  residues processed: 170
  average time/residue: 0.0533
  time to fit residues: 13.5303
Evaluate side-chains
  158 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  288 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 363 GLN
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.120016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.109332 restraints weight = 18733.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 4.18
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.4500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6282  Z= 0.144
  Angle     :  0.733   8.541   8506  Z= 0.362
  Chirality :  0.041   0.155    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.343  16.392    801
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 26.81 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.32 (0.55), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 441 
 TYR   0.009   0.001   TYR A 379 
 PHE   0.045   0.001   PHE A 470 
 TRP   0.012   0.001   TRP B 321 
 HIS   0.002   0.001   HIS B 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6282)
  covalent geometry    : angle       0.73268 ( 8506)
  hydrogen bonds       : bond        0.03587 (  346)
  hydrogen bonds       : angle       4.47242 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B  211 MET cc_start: 0.8600 (mmm) cc_final: 0.8054 (mmm)
REVERT: B  239 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8632 (tm-30)
REVERT: B  376 ILE cc_start: 0.6649 (mm) cc_final: 0.6245 (mm)
REVERT: B  437 PHE cc_start: 0.7959 (m-80) cc_final: 0.7681 (m-80)
REVERT: A  321 TRP cc_start: 0.8588 (t60) cc_final: 0.8135 (t60)
REVERT: A  359 MET cc_start: 0.7777 (ppp) cc_final: 0.7281 (ppp)
REVERT: A  363 GLN cc_start: 0.7802 (mt0) cc_final: 0.7378 (mt0)
REVERT: A  440 LEU cc_start: 0.7720 (mm) cc_final: 0.7451 (mm)
  outliers start: 22
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0546
  time to fit residues: 13.5108
Evaluate side-chains
  157 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  288 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.119512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.108640 restraints weight = 18765.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 4.23
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.4633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   6282  Z= 0.157
  Angle     :  0.799  12.617   8506  Z= 0.387
  Chirality :  0.044   0.166    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.482  17.441    801
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 27.89 %
    Favored  : 69.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.32), residues: 745
  helix:  0.51 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -1.55 (0.53), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  67 
 TYR   0.011   0.001   TYR A 379 
 PHE   0.044   0.002   PHE A 470 
 TRP   0.011   0.001   TRP B 474 
 HIS   0.003   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6282)
  covalent geometry    : angle       0.79872 ( 8506)
  hydrogen bonds       : bond        0.03748 (  346)
  hydrogen bonds       : angle       4.59370 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.243 
Fit side-chains
REVERT: B  211 MET cc_start: 0.8657 (mmm) cc_final: 0.8130 (mmm)
REVERT: B  376 ILE cc_start: 0.6595 (mm) cc_final: 0.6246 (mm)
REVERT: A   33 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8679 (pp)
REVERT: A  321 TRP cc_start: 0.8609 (t60) cc_final: 0.8142 (t60)
REVERT: A  328 GLU cc_start: 0.7532 (tp30) cc_final: 0.7155 (tt0)
REVERT: A  359 MET cc_start: 0.7782 (ppp) cc_final: 0.7303 (ppp)
REVERT: A  363 GLN cc_start: 0.7866 (mt0) cc_final: 0.7428 (mt0)
REVERT: A  440 LEU cc_start: 0.7857 (mm) cc_final: 0.7595 (mm)
  outliers start: 17
  outliers final: 13
  residues processed: 161
  average time/residue: 0.0553
  time to fit residues: 13.3354
Evaluate side-chains
  161 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  288 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0370
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    0.4980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.121535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.110679 restraints weight = 18411.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 4.24
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6282  Z= 0.145
  Angle     :  0.792  12.567   8506  Z= 0.380
  Chirality :  0.042   0.158    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.448  16.974    801
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 28.04 %
    Favored  : 69.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.32), residues: 745
  helix:  0.47 (0.22), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.43 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.012   0.001   TYR A 379 
 PHE   0.046   0.001   PHE A 470 
 TRP   0.009   0.001   TRP B  39 
 HIS   0.004   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6282)
  covalent geometry    : angle       0.79219 ( 8506)
  hydrogen bonds       : bond        0.03632 (  346)
  hydrogen bonds       : angle       4.57275 ( 1026)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.194 
Fit side-chains
REVERT: B  211 MET cc_start: 0.8615 (mmm) cc_final: 0.8090 (mmm)
REVERT: B  239 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: B  376 ILE cc_start: 0.6600 (mm) cc_final: 0.6164 (mm)
REVERT: A   33 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8669 (pp)
REVERT: A  321 TRP cc_start: 0.8606 (t60) cc_final: 0.8128 (t60)
REVERT: A  328 GLU cc_start: 0.7545 (tp30) cc_final: 0.7206 (tt0)
REVERT: A  363 GLN cc_start: 0.7827 (mt0) cc_final: 0.7169 (mm-40)
REVERT: A  440 LEU cc_start: 0.7797 (mm) cc_final: 0.7522 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 150
  average time/residue: 0.0555
  time to fit residues: 12.3714
Evaluate side-chains
  149 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  288 MET
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 64 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.121219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.110506 restraints weight = 18584.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 4.14
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.4795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6282  Z= 0.144
  Angle     :  0.805  13.108   8506  Z= 0.385
  Chirality :  0.042   0.152    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.378  16.315    801
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 27.58 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.32), residues: 745
  helix:  0.46 (0.22), residues: 582
  sheet:  None (None), residues: 0
  loop : -1.50 (0.55), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  45 
 TYR   0.016   0.001   TYR A 379 
 PHE   0.051   0.001   PHE A 470 
 TRP   0.009   0.001   TRP B  39 
 HIS   0.005   0.001   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6282)
  covalent geometry    : angle       0.80472 ( 8506)
  hydrogen bonds       : bond        0.03566 (  346)
  hydrogen bonds       : angle       4.48357 ( 1026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1417.33 seconds
wall clock time: 25 minutes 7.70 seconds (1507.70 seconds total)