Starting phenix.real_space_refine
on Thu Nov 14 11:53:34 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_11067.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_11067.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_11067.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_11067.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/11_2024/6z3z_11067.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 3.95, per 1000 atoms: 0.65
  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: 1.39
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.62
  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: 1.52

  Time building geometry restraints manager: 1.65 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:             0.680
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.230
  Find NCS groups from input model:        0.210
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.420
-------------------------------------------------------------------------------
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= 0.162
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.009   0.001   TRP A 429 
 HIS   0.003   0.001   HIS A 390 
 PHE   0.015   0.001   PHE B 377 
 TYR   0.011   0.001   TYR B 350 
 ARG   0.013   0.001   ARG A  45 

*********************** 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  : 0.677 
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: 0.1420
  time to fit residues: 35.1781
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  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
A 433 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6282  Z= 0.219
  Angle     :  0.696   9.921   8506  Z= 0.354
  Chirality :  0.040   0.146    981
  Planarity :  0.004   0.056   1032
  Dihedral  :  4.206  18.029    801
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.02 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.32), residues: 745
  helix:  0.48 (0.22), residues: 565
  sheet:  None (None), residues: 0
  loop : -1.68 (0.50), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 433 
 PHE   0.040   0.002   PHE A 470 
 TYR   0.016   0.001   TYR A 252 
 ARG   0.004   0.001   ARG A  45 

*********************** 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
  156 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 152
  time to evaluate  : 0.666 
Fit side-chains
REVERT: B  126 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8440 (tttt)
REVERT: B  362 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8272 (mttp)
REVERT: B  376 ILE cc_start: 0.6885 (mm) cc_final: 0.6251 (mt)
REVERT: A   31 LEU cc_start: 0.9401 (mp) cc_final: 0.9184 (mp)
REVERT: A   62 MET cc_start: 0.8352 (tpp) cc_final: 0.8128 (tpp)
REVERT: A  188 MET cc_start: 0.7610 (mmp) cc_final: 0.6880 (mmt)
REVERT: A  364 LEU cc_start: 0.9009 (tp) cc_final: 0.8809 (tt)
REVERT: A  440 LEU cc_start: 0.7671 (mm) cc_final: 0.7361 (mm)
  outliers start: 4
  outliers final: 3
  residues processed: 155
  average time/residue: 0.1343
  time to fit residues: 29.6154
Evaluate side-chains
  137 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   60 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 363 GLN
** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6282  Z= 0.227
  Angle     :  0.678   9.733   8506  Z= 0.342
  Chirality :  0.041   0.138    981
  Planarity :  0.004   0.057   1032
  Dihedral  :  4.430  16.902    801
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.87 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.32), residues: 745
  helix:  0.53 (0.22), residues: 571
  sheet:  None (None), residues: 0
  loop : -1.57 (0.53), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 429 
 HIS   0.004   0.001   HIS A 433 
 PHE   0.048   0.001   PHE A 470 
 TYR   0.013   0.001   TYR A 379 
 ARG   0.004   0.001   ARG A  45 

*********************** 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
  171 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.547 
Fit side-chains
REVERT: B   25 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8566 (pp)
REVERT: B  376 ILE cc_start: 0.6813 (mm) cc_final: 0.6055 (mt)
REVERT: B  454 GLU cc_start: 0.7762 (tp30) cc_final: 0.7521 (tp30)
REVERT: A  359 MET cc_start: 0.8027 (ppp) cc_final: 0.7293 (ppp)
REVERT: A  363 GLN cc_start: 0.7875 (mt0) cc_final: 0.7337 (mt0)
REVERT: A  440 LEU cc_start: 0.7753 (mm) cc_final: 0.7505 (mm)
  outliers start: 11
  outliers final: 7
  residues processed: 163
  average time/residue: 0.1330
  time to fit residues: 30.6108
Evaluate side-chains
  146 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain A residue   60 LEU
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 68 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 411 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6282  Z= 0.196
  Angle     :  0.680   9.643   8506  Z= 0.337
  Chirality :  0.040   0.154    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.342  17.051    801
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.03 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.32), residues: 745
  helix:  0.58 (0.22), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.36 (0.53), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 429 
 HIS   0.003   0.001   HIS A 433 
 PHE   0.042   0.001   PHE A 470 
 TYR   0.019   0.001   TYR A 379 
 ARG   0.003   0.000   ARG A  45 

*********************** 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
  166 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.710 
Fit side-chains
REVERT: B   25 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8573 (pp)
REVERT: B   31 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7453 (mp)
REVERT: B  376 ILE cc_start: 0.6732 (mm) cc_final: 0.5953 (mt)
REVERT: A  184 PHE cc_start: 0.8002 (p90) cc_final: 0.7789 (p90)
REVERT: A  188 MET cc_start: 0.7842 (mmp) cc_final: 0.7089 (mmt)
REVERT: A  359 MET cc_start: 0.7970 (ppp) cc_final: 0.7417 (ppp)
REVERT: A  363 GLN cc_start: 0.7771 (mt0) cc_final: 0.7430 (mt0)
REVERT: A  440 LEU cc_start: 0.7695 (mm) cc_final: 0.7433 (mm)
  outliers start: 18
  outliers final: 9
  residues processed: 157
  average time/residue: 0.1317
  time to fit residues: 29.7390
Evaluate side-chains
  150 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   31 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 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  133 ILE
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0170
   chunk 65 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.6620

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.3979

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= 0.187
  Angle     :  0.677  10.628   8506  Z= 0.334
  Chirality :  0.039   0.136    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.306  17.019    801
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.88 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.32), residues: 745
  helix:  0.64 (0.22), residues: 567
  sheet:  None (None), residues: 0
  loop : -1.10 (0.54), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 321 
 HIS   0.002   0.001   HIS A 145 
 PHE   0.038   0.001   PHE A 470 
 TYR   0.017   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

*********************** 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
  167 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 LEU cc_start: 0.7787 (mp) cc_final: 0.7123 (mp)
REVERT: B  376 ILE cc_start: 0.6567 (mm) cc_final: 0.6122 (mm)
REVERT: A   62 MET cc_start: 0.8488 (tpp) cc_final: 0.8279 (tpp)
REVERT: A  163 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8528 (mm)
REVERT: A  184 PHE cc_start: 0.7916 (p90) cc_final: 0.7663 (p90)
REVERT: A  321 TRP cc_start: 0.8388 (t60) cc_final: 0.8187 (t60)
REVERT: A  359 MET cc_start: 0.7915 (ppp) cc_final: 0.7199 (ppp)
REVERT: A  363 GLN cc_start: 0.7777 (mt0) cc_final: 0.7296 (mt0)
REVERT: A  434 MET cc_start: 0.7043 (tpt) cc_final: 0.6622 (mmm)
REVERT: A  440 LEU cc_start: 0.7688 (mm) cc_final: 0.7393 (mm)
  outliers start: 18
  outliers final: 9
  residues processed: 156
  average time/residue: 0.1341
  time to fit residues: 29.9287
Evaluate side-chains
  152 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  138 LEU
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 A residue   31 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  467 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   overall best weight:    1.3586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6282  Z= 0.235
  Angle     :  0.708  10.396   8506  Z= 0.351
  Chirality :  0.041   0.141    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.503  17.183    801
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 23.88 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.32), residues: 745
  helix:  0.61 (0.22), residues: 569
  sheet:  None (None), residues: 0
  loop : -1.31 (0.53), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 474 
 HIS   0.003   0.001   HIS B 145 
 PHE   0.041   0.002   PHE A 470 
 TYR   0.019   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

*********************** 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
  168 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8768 (pp)
REVERT: B   31 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7631 (mp)
REVERT: B  367 PHE cc_start: 0.8608 (t80) cc_final: 0.8344 (t80)
REVERT: B  376 ILE cc_start: 0.6643 (mm) cc_final: 0.6180 (mm)
REVERT: B  434 MET cc_start: 0.7584 (mpp) cc_final: 0.6994 (mtm)
REVERT: A  163 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8520 (mm)
REVERT: A  184 PHE cc_start: 0.7980 (p90) cc_final: 0.7581 (p90)
REVERT: A  188 MET cc_start: 0.7790 (mmp) cc_final: 0.7194 (mmt)
REVERT: A  235 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9143 (tp)
REVERT: A  363 GLN cc_start: 0.7867 (mt0) cc_final: 0.7372 (mt0)
REVERT: A  395 LEU cc_start: 0.7595 (pt) cc_final: 0.7348 (pp)
REVERT: A  434 MET cc_start: 0.7043 (tpt) cc_final: 0.6583 (mmm)
REVERT: A  440 LEU cc_start: 0.7808 (mm) cc_final: 0.7548 (mm)
  outliers start: 20
  outliers final: 12
  residues processed: 159
  average time/residue: 0.1223
  time to fit residues: 27.9308
Evaluate side-chains
  159 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   31 LEU
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  279 LEU
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  133 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  290 SER
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 8 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 43 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.4534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6282  Z= 0.238
  Angle     :  0.734   9.286   8506  Z= 0.361
  Chirality :  0.042   0.170    981
  Planarity :  0.004   0.058   1032
  Dihedral  :  4.601  18.167    801
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.04 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.32), residues: 745
  helix:  0.51 (0.22), residues: 571
  sheet:  None (None), residues: 0
  loop : -1.26 (0.54), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 474 
 HIS   0.003   0.001   HIS B 145 
 PHE   0.042   0.001   PHE A 470 
 TYR   0.027   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

*********************** 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
  180 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 0.642 
Fit side-chains
REVERT: B  367 PHE cc_start: 0.8669 (t80) cc_final: 0.8394 (t80)
REVERT: B  376 ILE cc_start: 0.6458 (mm) cc_final: 0.6056 (mm)
REVERT: B  434 MET cc_start: 0.7620 (mpp) cc_final: 0.7016 (mtm)
REVERT: A   33 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8748 (pp)
REVERT: A  163 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8529 (mm)
REVERT: A  359 MET cc_start: 0.7876 (ppp) cc_final: 0.7251 (ppp)
REVERT: A  363 GLN cc_start: 0.7895 (mt0) cc_final: 0.7466 (mt0)
REVERT: A  434 MET cc_start: 0.6746 (tpt) cc_final: 0.6444 (mmm)
REVERT: A  437 PHE cc_start: 0.7800 (m-80) cc_final: 0.7465 (m-80)
REVERT: A  440 LEU cc_start: 0.7955 (mm) cc_final: 0.7700 (mm)
  outliers start: 25
  outliers final: 14
  residues processed: 167
  average time/residue: 0.1295
  time to fit residues: 30.8633
Evaluate side-chains
  164 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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  138 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  380 MET
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  133 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  310 MET
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 14 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 70 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 433 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6282  Z= 0.216
  Angle     :  0.752   8.661   8506  Z= 0.369
  Chirality :  0.042   0.229    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.564  18.108    801
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 26.35 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.32), residues: 745
  helix:  0.42 (0.22), residues: 574
  sheet:  None (None), residues: 0
  loop : -1.39 (0.54), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  39 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.041   0.001   PHE A 470 
 TYR   0.024   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

*********************** 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
  176 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  239 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8653 (tm-30)
REVERT: B  376 ILE cc_start: 0.6367 (mm) cc_final: 0.6072 (mm)
REVERT: B  434 MET cc_start: 0.7582 (mpp) cc_final: 0.7038 (mtm)
REVERT: A   33 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8761 (pp)
REVERT: A  163 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8453 (mm)
REVERT: A  211 MET cc_start: 0.7617 (mmm) cc_final: 0.7146 (mmm)
REVERT: A  359 MET cc_start: 0.7922 (ppp) cc_final: 0.7328 (ppp)
REVERT: A  363 GLN cc_start: 0.7908 (mt0) cc_final: 0.7496 (mt0)
REVERT: A  440 LEU cc_start: 0.7942 (mm) cc_final: 0.7661 (mm)
  outliers start: 20
  outliers final: 15
  residues processed: 165
  average time/residue: 0.1377
  time to fit residues: 32.3196
Evaluate side-chains
  165 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  138 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  380 MET
Chi-restraints excluded: chain B residue  390 HIS
Chi-restraints excluded: chain B residue  430 ASN
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  290 SER
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 29 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6282  Z= 0.222
  Angle     :  0.763   8.477   8506  Z= 0.374
  Chirality :  0.042   0.176    981
  Planarity :  0.004   0.059   1032
  Dihedral  :  4.531  18.212    801
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 27.12 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.32), residues: 745
  helix:  0.45 (0.22), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.48 (0.55), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 321 
 HIS   0.003   0.001   HIS A 145 
 PHE   0.045   0.001   PHE A 470 
 TYR   0.023   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

*********************** 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
  173 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  211 MET cc_start: 0.8760 (mmm) cc_final: 0.8367 (mmm)
REVERT: B  376 ILE cc_start: 0.6389 (mm) cc_final: 0.6042 (mm)
REVERT: B  387 PHE cc_start: 0.7946 (t80) cc_final: 0.7647 (t80)
REVERT: B  434 MET cc_start: 0.7547 (mpp) cc_final: 0.7027 (mtm)
REVERT: A   33 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8754 (pp)
REVERT: A  163 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8635 (mm)
REVERT: A  211 MET cc_start: 0.7576 (mmm) cc_final: 0.7210 (mmm)
REVERT: A  359 MET cc_start: 0.7975 (ppp) cc_final: 0.7450 (ppp)
REVERT: A  363 GLN cc_start: 0.7949 (mt0) cc_final: 0.7545 (mt0)
REVERT: A  434 MET cc_start: 0.6521 (tpt) cc_final: 0.6268 (tpt)
REVERT: A  440 LEU cc_start: 0.8134 (mm) cc_final: 0.7851 (mm)
  outliers start: 18
  outliers final: 13
  residues processed: 164
  average time/residue: 0.1333
  time to fit residues: 31.2026
Evaluate side-chains
  163 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  390 HIS
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  163 LEU
Chi-restraints excluded: chain A residue  290 SER
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 69 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   6282  Z= 0.227
  Angle     :  0.788   8.666   8506  Z= 0.387
  Chirality :  0.043   0.167    981
  Planarity :  0.005   0.060   1032
  Dihedral  :  4.599  19.162    801
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 27.43 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.32), residues: 745
  helix:  0.42 (0.22), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.62 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 321 
 HIS   0.002   0.001   HIS A 145 
 PHE   0.046   0.002   PHE A 470 
 TYR   0.021   0.001   TYR A 379 
 ARG   0.002   0.000   ARG A  45 

********************** 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
  168 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  211 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8338 (mmm)
REVERT: B  239 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: B  376 ILE cc_start: 0.6353 (mm) cc_final: 0.5961 (mm)
REVERT: B  387 PHE cc_start: 0.7973 (t80) cc_final: 0.7666 (t80)
REVERT: A   33 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8742 (pp)
REVERT: A  163 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8449 (mm)
REVERT: A  211 MET cc_start: 0.7607 (mmm) cc_final: 0.7273 (mmm)
REVERT: A  359 MET cc_start: 0.7971 (ppp) cc_final: 0.7454 (ppp)
REVERT: A  363 GLN cc_start: 0.7955 (mt0) cc_final: 0.7544 (mt0)
REVERT: A  434 MET cc_start: 0.6584 (tpt) cc_final: 0.6335 (tpt)
REVERT: A  440 LEU cc_start: 0.8143 (mm) cc_final: 0.7835 (mm)
  outliers start: 19
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1224
  time to fit residues: 27.7843
Evaluate side-chains
  159 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   27 PHE
Chi-restraints excluded: chain B residue   65 ILE
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  211 MET
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  390 HIS
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  163 LEU
Chi-restraints excluded: chain A residue  290 SER
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 60 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 3 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: