Starting phenix.real_space_refine
on Tue Mar  3 22:01:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dmo_27545/03_2026/8dmo_27545.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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      54      5.16       5
     C    5649      2.51       5
     N    1549      2.21       5
     O    1660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8912
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4459
          Classifications: {'peptide': 575}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4453
          Classifications: {'peptide': 575}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 561}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 2.19, per 1000 atoms: 0.25
  Number of scatterers: 8912
  At special positions: 0
  Unit cell: (89.46, 136.32, 136.32, 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      54     16.00
     O    1660      8.00
     N    1549      7.00
     C    5649      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: 0.74
  Conformation dependent library (CDL) restraints added in 339.6 milliseconds
  

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      71.2% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.570A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
      removed outlier: 3.580A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 109
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 4.278A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 3.773A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 130 through 164
    Processing helix  chain 'A' and resid 164 through 212
      Proline residue:  A 176  - end of helix
      removed outlier: 4.233A  pdb=" N   GLN A 202 " --> pdb=" O   ASN A 198 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL A 203 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   SER A 206 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   GLU A 208 " --> pdb=" O   THR A 204 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   MET A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
      removed outlier: 3.748A  pdb=" N   ILE A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 272
      removed outlier: 4.441A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.836A  pdb=" N   PHE A 272 " --> pdb=" O   TYR A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.818A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 302
      removed outlier: 4.537A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.563A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 323
      removed outlier: 3.585A  pdb=" N   GLN A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.928A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 4.090A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 464
      removed outlier: 3.545A  pdb=" N   ASN A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.532A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 497
      removed outlier: 3.618A  pdb=" N   ARG A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.973A  pdb=" N   ILE A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN A 527 " --> pdb=" O   LEU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 578
    Processing helix  chain 'B' and resid 8 through 21
      removed outlier: 3.649A  pdb=" N   THR B  12 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 3.599A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.681A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 113 through 119
      removed outlier: 3.545A  pdb=" N   GLN B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 130
      removed outlier: 3.756A  pdb=" N   ILE B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 200
      removed outlier: 8.040A  pdb=" N   GLN B 166 " --> pdb=" O   TYR B 162 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   LEU B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LEU B 174 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA B 175 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 200 through 212
      removed outlier: 4.056A  pdb=" N   THR B 204 " --> pdb=" O   MET B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 5.161A  pdb=" N   ILE B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 221 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
      removed outlier: 3.598A  pdb=" N   GLN B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 270
      removed outlier: 3.641A  pdb=" N   ILE B 254 " --> pdb=" O   ILE B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 277
      removed outlier: 3.811A  pdb=" N   ASP B 277 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 302
      removed outlier: 3.725A  pdb=" N   ILE B 284 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   THR B 285 " --> pdb=" O   ALA B 281 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   SER B 289 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.618A  pdb=" N   GLN B 307 " --> pdb=" O   ASN B 303 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
      removed outlier: 3.724A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
      removed outlier: 3.869A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 445
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.631A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 497
    Processing helix  chain 'B' and resid 515 through 527
      removed outlier: 3.818A  pdb=" N   ILE B 519 " --> pdb=" O   SER B 515 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN B 527 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 578
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 6.401A  pdb=" N   ARG A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   GLU A 399 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.239A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLU A 552 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   ILE A 556 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 366
      removed outlier: 6.548A  pdb=" N   ARG B 360 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   THR B 348 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   ILE B 362 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.544A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    574 hydrogen bonds defined for protein.
    1677 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: 1.28

  Time building geometry restraints manager: 0.99 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: 2951
        1.34 -     1.46: 1909
        1.46 -     1.58: 4080
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 9044
  Sorted by residual:
  bond pdb=" N   ILE B 172 "
       pdb=" CA  ILE B 172 "
    ideal  model  delta    sigma   weight residual
    1.459  1.440  0.019 1.25e-02 6.40e+03 2.37e+00
  bond pdb=" C   VAL A 356 "
       pdb=" N   PRO A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.015 1.19e-02 7.06e+03 1.66e+00
  bond pdb=" CB  PRO A 297 "
       pdb=" CG  PRO A 297 "
    ideal  model  delta    sigma   weight residual
    1.492  1.446  0.046 5.00e-02 4.00e+02 8.34e-01
  bond pdb=" CB  GLU B 336 "
       pdb=" CG  GLU B 336 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.36e-01
  bond pdb=" N   VAL B 173 "
       pdb=" CA  VAL B 173 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.011 1.25e-02 6.40e+03 7.11e-01
  ... (remaining 9039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11996
        1.88 -     3.76: 181
        3.76 -     5.64: 35
        5.64 -     7.52: 6
        7.52 -     9.40: 5
  Bond angle restraints: 12223
  Sorted by residual:
  angle pdb=" C   ILE B 172 "
        pdb=" N   VAL B 173 "
        pdb=" CA  VAL B 173 "
      ideal   model   delta    sigma   weight residual
     121.97  127.75   -5.78 1.80e+00 3.09e-01 1.03e+01
  angle pdb=" CB  MET B 111 "
        pdb=" CG  MET B 111 "
        pdb=" SD  MET B 111 "
      ideal   model   delta    sigma   weight residual
     112.70  103.30    9.40 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" CA  MET B 466 "
        pdb=" CB  MET B 466 "
        pdb=" CG  MET B 466 "
      ideal   model   delta    sigma   weight residual
     114.10  120.27   -6.17 2.00e+00 2.50e-01 9.51e+00
  angle pdb=" CB  MET B 196 "
        pdb=" CG  MET B 196 "
        pdb=" SD  MET B 196 "
      ideal   model   delta    sigma   weight residual
     112.70  121.56   -8.86 3.00e+00 1.11e-01 8.71e+00
  angle pdb=" CA  MET A 466 "
        pdb=" CB  MET A 466 "
        pdb=" CG  MET A 466 "
      ideal   model   delta    sigma   weight residual
     114.10  120.00   -5.90 2.00e+00 2.50e-01 8.70e+00
  ... (remaining 12218 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4942
       17.92 -    35.85: 458
       35.85 -    53.77: 72
       53.77 -    71.70: 17
       71.70 -    89.62: 10
  Dihedral angle restraints: 5499
    sinusoidal: 2177
      harmonic: 3322
  Sorted by residual:
  dihedral pdb=" CA  MET B 111 "
           pdb=" C   MET B 111 "
           pdb=" N   PRO B 112 "
           pdb=" CA  PRO B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.69  -26.31     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  MET A 466 "
           pdb=" C   MET A 466 "
           pdb=" N   ASP A 467 "
           pdb=" CA  ASP A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  MET B 466 "
           pdb=" C   MET B 466 "
           pdb=" N   ASP B 467 "
           pdb=" CA  ASP B 467 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.63  -18.37     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5496 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 921
       0.033 -    0.066: 361
       0.066 -    0.099: 119
       0.099 -    0.132: 49
       0.132 -    0.165: 4
  Chirality restraints: 1454
  Sorted by residual:
  chirality pdb=" CB  ILE A 501 "
            pdb=" CA  ILE A 501 "
            pdb=" CG1 ILE A 501 "
            pdb=" CG2 ILE A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.82e-01
  chirality pdb=" CA  TRP B  17 "
            pdb=" N   TRP B  17 "
            pdb=" C   TRP B  17 "
            pdb=" CB  TRP B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  MET A 109 "
            pdb=" N   MET A 109 "
            pdb=" C   MET A 109 "
            pdb=" CB  MET A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.32e-01
  ... (remaining 1451 not shown)

  Planarity restraints: 1547
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 296 "   -0.028 5.00e-02 4.00e+02   4.24e-02 2.87e+00
        pdb=" N   PRO A 297 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 297 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 297 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 296 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO B 297 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 252 "   -0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO A 253 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 253 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 253 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1544 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1636
        2.77 -     3.30: 9524
        3.30 -     3.84: 14652
        3.84 -     4.37: 15871
        4.37 -     4.90: 27705
  Nonbonded interactions: 69388
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  46 "
            pdb=" OH  TYR B 163 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG1 THR B  12 "
            pdb=" OE1 GLN B 316 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OH  TYR B 351 "
            pdb=" OG1 THR B 384 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   THR A 280 "
            pdb=" OG1 THR A 283 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN B 363 "
            pdb=" NH2 ARG B 559 "
     model   vdw
     2.267 3.120
  ... (remaining 69383 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' and (resid 7 through 496 or (resid 497 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 498 through 581))
  selection = chain 'B'
}

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 group one per residue
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:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.060
  Find NCS groups from input model:        0.120
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
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   0.046   9044  Z= 0.142
  Angle     :  0.626   9.395  12223  Z= 0.324
  Chirality :  0.042   0.165   1454
  Planarity :  0.004   0.042   1547
  Dihedral  : 14.363  89.619   3351
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.97 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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:  1.78 (0.25), residues: 1146
  helix:  2.06 (0.20), residues: 682
  sheet:  1.07 (0.61), residues: 76
  loop : -0.37 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.017   0.002   PHE B 115 
 TRP   0.009   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 9044)
  covalent geometry    : angle       0.62555 (12223)
  hydrogen bonds       : bond        0.13514 (  574)
  hydrogen bonds       : angle       4.96911 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1042
  time to fit residues: 14.4308
Evaluate side-chains
  67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
A 326 GLN
A 436 ASN
A 520 GLN
B 436 ASN
B 520 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.035654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.025645 restraints weight = 81766.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.026471 restraints weight = 51228.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.027015 restraints weight = 38157.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.027429 restraints weight = 31407.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.027707 restraints weight = 27364.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9044  Z= 0.139
  Angle     :  0.608   9.283  12223  Z= 0.310
  Chirality :  0.041   0.135   1454
  Planarity :  0.004   0.041   1547
  Dihedral  :  3.859  19.583   1249
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.97 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.31 %
    Favored  : 89.87 %
  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:  1.89 (0.25), residues: 1146
  helix:  1.99 (0.20), residues: 728
  sheet:  1.64 (0.60), residues: 70
  loop : -0.40 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 455 
 TYR   0.010   0.001   TYR B 439 
 PHE   0.011   0.001   PHE A 462 
 TRP   0.009   0.001   TRP B  10 
 HIS   0.004   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9044)
  covalent geometry    : angle       0.60826 (12223)
  hydrogen bonds       : bond        0.04145 (  574)
  hydrogen bonds       : angle       4.36465 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9442 (tpp) cc_final: 0.9116 (mmp)
REVERT: A   98 MET cc_start: 0.9160 (tpp) cc_final: 0.8556 (tpp)
REVERT: A  160 MET cc_start: 0.9610 (mtm) cc_final: 0.9225 (mtp)
REVERT: A  196 MET cc_start: 0.9375 (tpp) cc_final: 0.8501 (tpp)
REVERT: A  200 MET cc_start: 0.9475 (tpp) cc_final: 0.8824 (mpp)
REVERT: A  276 MET cc_start: 0.8854 (ptm) cc_final: 0.8536 (ptm)
REVERT: B   98 MET cc_start: 0.9135 (ttm) cc_final: 0.8689 (tpp)
REVERT: B  111 MET cc_start: 0.9379 (tmm) cc_final: 0.9044 (tmm)
REVERT: B  160 MET cc_start: 0.9529 (ttm) cc_final: 0.9307 (ttm)
REVERT: B  196 MET cc_start: 0.9470 (tpt) cc_final: 0.7774 (tpp)
REVERT: B  210 MET cc_start: 0.9253 (mmm) cc_final: 0.8974 (mmt)
REVERT: B  244 MET cc_start: 0.9789 (ttm) cc_final: 0.9025 (ttt)
REVERT: B  402 MET cc_start: 0.9147 (ppp) cc_final: 0.8929 (ppp)
REVERT: B  466 MET cc_start: 0.8533 (tmm) cc_final: 0.8330 (ppp)
  outliers start: 8
  outliers final: 3
  residues processed: 79
  average time/residue: 0.0918
  time to fit residues: 10.4249
Evaluate side-chains
  70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 62 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.036406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.025980 restraints weight = 81648.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.026745 restraints weight = 53821.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.027304 restraints weight = 41291.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.027685 restraints weight = 34359.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.027954 restraints weight = 30285.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9044  Z= 0.115
  Angle     :  0.556   8.806  12223  Z= 0.283
  Chirality :  0.040   0.184   1454
  Planarity :  0.003   0.038   1547
  Dihedral  :  3.698  16.142   1249
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.79 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 13.92 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.02 (0.25), residues: 1146
  helix:  2.07 (0.19), residues: 732
  sheet:  1.63 (0.60), residues: 70
  loop : -0.29 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 530 
 TYR   0.031   0.001   TYR A 572 
 PHE   0.008   0.001   PHE B 392 
 TRP   0.008   0.001   TRP B  10 
 HIS   0.003   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9044)
  covalent geometry    : angle       0.55572 (12223)
  hydrogen bonds       : bond        0.03740 (  574)
  hydrogen bonds       : angle       4.20398 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9549 (tpp) cc_final: 0.9053 (mmp)
REVERT: A   98 MET cc_start: 0.9051 (tpp) cc_final: 0.8542 (tpt)
REVERT: A  111 MET cc_start: 0.8587 (tmm) cc_final: 0.8241 (tmm)
REVERT: A  160 MET cc_start: 0.9664 (mtm) cc_final: 0.9234 (mtt)
REVERT: A  196 MET cc_start: 0.9470 (tpp) cc_final: 0.8153 (tpp)
REVERT: A  200 MET cc_start: 0.9574 (tpp) cc_final: 0.9001 (tpp)
REVERT: A  244 MET cc_start: 0.9500 (mtt) cc_final: 0.8729 (mmt)
REVERT: A  276 MET cc_start: 0.8884 (ptm) cc_final: 0.8417 (ptm)
REVERT: A  460 MET cc_start: 0.9224 (mmm) cc_final: 0.8738 (mmm)
REVERT: B   98 MET cc_start: 0.9143 (ttm) cc_final: 0.8663 (tpp)
REVERT: B  111 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8881 (tmm)
REVERT: B  196 MET cc_start: 0.9560 (tpt) cc_final: 0.8636 (tpp)
REVERT: B  200 MET cc_start: 0.8958 (mmm) cc_final: 0.8029 (mmm)
REVERT: B  210 MET cc_start: 0.9301 (mmm) cc_final: 0.8992 (mmt)
REVERT: B  244 MET cc_start: 0.9766 (ttm) cc_final: 0.8769 (ttt)
REVERT: B  402 MET cc_start: 0.9152 (ppp) cc_final: 0.8814 (ppp)
  outliers start: 5
  outliers final: 3
  residues processed: 72
  average time/residue: 0.0922
  time to fit residues: 9.4117
Evaluate side-chains
  71 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 109 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 202 GLN
B 209 GLN
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.032891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.023345 restraints weight = 85458.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.024077 restraints weight = 54633.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.024574 restraints weight = 41185.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.024939 restraints weight = 34080.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.025185 restraints weight = 29890.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9044  Z= 0.230
  Angle     :  0.634   9.322  12223  Z= 0.330
  Chirality :  0.041   0.143   1454
  Planarity :  0.004   0.041   1547
  Dihedral  :  3.922  16.687   1249
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.93 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.66 %
    Favored  : 82.91 %
  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:  1.65 (0.25), residues: 1146
  helix:  1.66 (0.19), residues: 764
  sheet:  1.32 (0.60), residues: 70
  loop : -0.29 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 455 
 TYR   0.024   0.002   TYR A 572 
 PHE   0.015   0.002   PHE B 392 
 TRP   0.010   0.001   TRP B  66 
 HIS   0.007   0.002   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 9044)
  covalent geometry    : angle       0.63419 (12223)
  hydrogen bonds       : bond        0.03982 (  574)
  hydrogen bonds       : angle       4.54899 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9512 (tpp) cc_final: 0.9120 (mmp)
REVERT: A   98 MET cc_start: 0.8969 (tpp) cc_final: 0.8444 (tpt)
REVERT: A  111 MET cc_start: 0.8902 (tmm) cc_final: 0.8601 (tmm)
REVERT: A  196 MET cc_start: 0.9511 (tpp) cc_final: 0.9200 (tpp)
REVERT: A  200 MET cc_start: 0.9540 (tpp) cc_final: 0.9280 (tpp)
REVERT: A  276 MET cc_start: 0.8878 (ptm) cc_final: 0.8369 (ptm)
REVERT: B   98 MET cc_start: 0.9126 (ttm) cc_final: 0.8817 (ttm)
REVERT: B  111 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.8890 (ppp)
REVERT: B  160 MET cc_start: 0.9641 (ttm) cc_final: 0.9325 (mmt)
REVERT: B  196 MET cc_start: 0.9525 (tpt) cc_final: 0.8313 (tpp)
REVERT: B  200 MET cc_start: 0.9034 (mmm) cc_final: 0.8104 (mmm)
REVERT: B  244 MET cc_start: 0.9729 (ttm) cc_final: 0.8562 (ttt)
REVERT: B  312 MET cc_start: 0.9305 (tpp) cc_final: 0.8622 (mmm)
REVERT: B  402 MET cc_start: 0.9177 (ppp) cc_final: 0.8920 (ppp)
  outliers start: 14
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0795
  time to fit residues: 8.2175
Evaluate side-chains
  67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  111 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.2997 r_free = 0.2997 target = 0.033050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.023639 restraints weight = 83768.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.024379 restraints weight = 53657.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.024897 restraints weight = 40300.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.025243 restraints weight = 33253.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.025511 restraints weight = 29177.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9044  Z= 0.178
  Angle     :  0.589   9.465  12223  Z= 0.302
  Chirality :  0.040   0.154   1454
  Planarity :  0.003   0.039   1547
  Dihedral  :  3.798  16.712   1249
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.05 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.30 %
    Favored  : 81.17 %
  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:  1.81 (0.25), residues: 1146
  helix:  1.88 (0.19), residues: 750
  sheet:  1.28 (0.60), residues: 70
  loop : -0.39 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.017   0.001   TYR A 572 
 PHE   0.012   0.001   PHE B  56 
 TRP   0.007   0.001   TRP B  10 
 HIS   0.007   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9044)
  covalent geometry    : angle       0.58900 (12223)
  hydrogen bonds       : bond        0.03798 (  574)
  hydrogen bonds       : angle       4.31791 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9508 (tpp) cc_final: 0.9135 (mmp)
REVERT: A   98 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8454 (tpt)
REVERT: A  111 MET cc_start: 0.8963 (tmm) cc_final: 0.8589 (tmm)
REVERT: A  196 MET cc_start: 0.9572 (tpp) cc_final: 0.9002 (tpp)
REVERT: A  200 MET cc_start: 0.9509 (tpp) cc_final: 0.9059 (tpp)
REVERT: A  276 MET cc_start: 0.8919 (ptm) cc_final: 0.8441 (ptm)
REVERT: A  460 MET cc_start: 0.9211 (mmm) cc_final: 0.8772 (mmm)
REVERT: B   98 MET cc_start: 0.9136 (ttm) cc_final: 0.8782 (ttm)
REVERT: B  196 MET cc_start: 0.9521 (tpt) cc_final: 0.8209 (tpp)
REVERT: B  200 MET cc_start: 0.9158 (mmm) cc_final: 0.7920 (mmm)
REVERT: B  244 MET cc_start: 0.9716 (ttm) cc_final: 0.8608 (ttm)
REVERT: B  312 MET cc_start: 0.9339 (tpp) cc_final: 0.8582 (mmm)
REVERT: B  402 MET cc_start: 0.9187 (ppp) cc_final: 0.8931 (ppp)
  outliers start: 15
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0754
  time to fit residues: 7.8350
Evaluate side-chains
  67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 109 optimal weight:    0.0870
   chunk 54 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.3012 r_free = 0.3012 target = 0.033496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.023662 restraints weight = 83436.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.024434 restraints weight = 53003.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.024976 restraints weight = 39678.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.025349 restraints weight = 32705.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.025631 restraints weight = 28654.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9044  Z= 0.137
  Angle     :  0.564   9.368  12223  Z= 0.285
  Chirality :  0.040   0.156   1454
  Planarity :  0.003   0.039   1547
  Dihedral  :  3.708  12.956   1249
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.23 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.20 %
    Favored  : 81.06 %
  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:  1.96 (0.25), residues: 1146
  helix:  2.00 (0.19), residues: 750
  sheet:  1.39 (0.60), residues: 70
  loop : -0.37 (0.36), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 102 
 TYR   0.015   0.001   TYR A 572 
 PHE   0.011   0.001   PHE B  56 
 TRP   0.008   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9044)
  covalent geometry    : angle       0.56398 (12223)
  hydrogen bonds       : bond        0.03664 (  574)
  hydrogen bonds       : angle       4.17561 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9522 (tpp) cc_final: 0.9155 (mmp)
REVERT: A   98 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8501 (tpt)
REVERT: A  111 MET cc_start: 0.8938 (tmm) cc_final: 0.8516 (tmm)
REVERT: A  196 MET cc_start: 0.9611 (tpp) cc_final: 0.9026 (tpp)
REVERT: A  200 MET cc_start: 0.9505 (tpp) cc_final: 0.9041 (tpp)
REVERT: A  223 GLN cc_start: 0.9422 (OUTLIER) cc_final: 0.9126 (mp10)
REVERT: A  276 MET cc_start: 0.8935 (ptm) cc_final: 0.8459 (ptm)
REVERT: B   98 MET cc_start: 0.9129 (ttm) cc_final: 0.8753 (ttm)
REVERT: B  196 MET cc_start: 0.9503 (tpt) cc_final: 0.8205 (tpp)
REVERT: B  200 MET cc_start: 0.9176 (mmm) cc_final: 0.8236 (mmm)
REVERT: B  244 MET cc_start: 0.9754 (ttm) cc_final: 0.8493 (ttt)
REVERT: B  312 MET cc_start: 0.9379 (tpp) cc_final: 0.8664 (mmm)
REVERT: B  402 MET cc_start: 0.9250 (ppp) cc_final: 0.8740 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0804
  time to fit residues: 9.0289
Evaluate side-chains
  71 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0040
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.5596

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.3010 r_free = 0.3010 target = 0.033513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.023687 restraints weight = 82664.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.024450 restraints weight = 52856.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.024955 restraints weight = 39716.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.025345 restraints weight = 33128.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.025606 restraints weight = 28882.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9044  Z= 0.138
  Angle     :  0.597  12.768  12223  Z= 0.297
  Chirality :  0.040   0.190   1454
  Planarity :  0.003   0.043   1547
  Dihedral  :  3.695  13.194   1249
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.79 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 18.01 %
    Favored  : 80.25 %
  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:  1.91 (0.25), residues: 1146
  helix:  1.94 (0.19), residues: 758
  sheet:  1.44 (0.62), residues: 70
  loop : -0.39 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 101 
 TYR   0.013   0.001   TYR A 572 
 PHE   0.009   0.001   PHE B 429 
 TRP   0.007   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9044)
  covalent geometry    : angle       0.59684 (12223)
  hydrogen bonds       : bond        0.03652 (  574)
  hydrogen bonds       : angle       4.17399 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9516 (tpp) cc_final: 0.9171 (mmp)
REVERT: A   98 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8492 (tpt)
REVERT: A  196 MET cc_start: 0.9628 (tpp) cc_final: 0.9368 (tpp)
REVERT: A  200 MET cc_start: 0.9506 (tpp) cc_final: 0.9265 (tpp)
REVERT: A  223 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.9147 (mp10)
REVERT: A  276 MET cc_start: 0.8938 (ptm) cc_final: 0.8467 (ptm)
REVERT: A  460 MET cc_start: 0.9322 (mmm) cc_final: 0.9013 (mmm)
REVERT: B   98 MET cc_start: 0.9122 (ttm) cc_final: 0.8755 (ttm)
REVERT: B  111 MET cc_start: 0.9802 (ttp) cc_final: 0.9227 (tmm)
REVERT: B  196 MET cc_start: 0.9491 (tpt) cc_final: 0.8187 (tpp)
REVERT: B  200 MET cc_start: 0.9218 (mmm) cc_final: 0.8307 (mmm)
REVERT: B  244 MET cc_start: 0.9765 (ttm) cc_final: 0.8520 (ttt)
REVERT: B  312 MET cc_start: 0.9389 (tpp) cc_final: 0.8670 (mmm)
REVERT: B  402 MET cc_start: 0.9268 (ppp) cc_final: 0.8828 (ppp)
  outliers start: 17
  outliers final: 10
  residues processed: 77
  average time/residue: 0.0827
  time to fit residues: 9.5457
Evaluate side-chains
  72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  543 GLU
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0060
   chunk 57 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 110 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.1202

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.2999 r_free = 0.2999 target = 0.032990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.023302 restraints weight = 84398.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.024047 restraints weight = 54942.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.024564 restraints weight = 41677.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.024911 restraints weight = 34640.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.025174 restraints weight = 30505.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9044  Z= 0.166
  Angle     :  0.624  11.088  12223  Z= 0.312
  Chirality :  0.041   0.199   1454
  Planarity :  0.003   0.042   1547
  Dihedral  :  3.845  18.050   1249
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.32 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.73 %
    Favored  : 79.73 %
  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:  1.85 (0.25), residues: 1146
  helix:  1.89 (0.19), residues: 758
  sheet:  1.41 (0.62), residues: 70
  loop : -0.39 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 101 
 TYR   0.014   0.001   TYR A 572 
 PHE   0.011   0.001   PHE B  56 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9044)
  covalent geometry    : angle       0.62411 (12223)
  hydrogen bonds       : bond        0.03704 (  574)
  hydrogen bonds       : angle       4.30078 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9508 (tpp) cc_final: 0.9180 (mmp)
REVERT: A   98 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8515 (tpt)
REVERT: A  111 MET cc_start: 0.8921 (tmm) cc_final: 0.8685 (tmm)
REVERT: A  196 MET cc_start: 0.9642 (tpp) cc_final: 0.9385 (tpp)
REVERT: A  223 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.9093 (mp10)
REVERT: A  276 MET cc_start: 0.8913 (ptm) cc_final: 0.8458 (ptm)
REVERT: A  312 MET cc_start: 0.9354 (mmm) cc_final: 0.8854 (tpp)
REVERT: A  402 MET cc_start: 0.9466 (ppp) cc_final: 0.9184 (ppp)
REVERT: B   44 MET cc_start: 0.9148 (tmm) cc_final: 0.8918 (tmm)
REVERT: B   98 MET cc_start: 0.9146 (ttm) cc_final: 0.8800 (ttm)
REVERT: B  111 MET cc_start: 0.9797 (ttp) cc_final: 0.9211 (tmm)
REVERT: B  196 MET cc_start: 0.9481 (tpt) cc_final: 0.8139 (tpp)
REVERT: B  200 MET cc_start: 0.9224 (mmm) cc_final: 0.8348 (mmm)
REVERT: B  244 MET cc_start: 0.9757 (ttm) cc_final: 0.8546 (ttt)
REVERT: B  312 MET cc_start: 0.9401 (tpp) cc_final: 0.8678 (mmm)
REVERT: B  402 MET cc_start: 0.9264 (ppp) cc_final: 0.8811 (ppp)
  outliers start: 15
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0732
  time to fit residues: 8.1595
Evaluate side-chains
  71 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 102 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.3017 r_free = 0.3017 target = 0.033666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.023820 restraints weight = 82678.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.024581 restraints weight = 53366.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.025111 restraints weight = 40271.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.025481 restraints weight = 33298.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.025761 restraints weight = 29203.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9044  Z= 0.125
  Angle     :  0.636  11.886  12223  Z= 0.310
  Chirality :  0.041   0.183   1454
  Planarity :  0.003   0.041   1547
  Dihedral  :  3.749  15.582   1249
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.44 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 19.45 %
    Favored  : 79.32 %
  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:  2.03 (0.25), residues: 1146
  helix:  2.06 (0.19), residues: 746
  sheet:  1.50 (0.62), residues: 70
  loop : -0.32 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 101 
 TYR   0.012   0.001   TYR A 572 
 PHE   0.012   0.001   PHE A 288 
 TRP   0.007   0.001   TRP B  10 
 HIS   0.004   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9044)
  covalent geometry    : angle       0.63562 (12223)
  hydrogen bonds       : bond        0.03635 (  574)
  hydrogen bonds       : angle       4.18746 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9531 (tpp) cc_final: 0.9185 (mmp)
REVERT: A   98 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8555 (tpt)
REVERT: A  111 MET cc_start: 0.8881 (tmm) cc_final: 0.8626 (tmm)
REVERT: A  196 MET cc_start: 0.9648 (tpp) cc_final: 0.9376 (tpp)
REVERT: A  223 GLN cc_start: 0.9418 (OUTLIER) cc_final: 0.9177 (mp10)
REVERT: A  276 MET cc_start: 0.8872 (ptm) cc_final: 0.8437 (ptm)
REVERT: A  312 MET cc_start: 0.9371 (mmm) cc_final: 0.8839 (tpp)
REVERT: A  402 MET cc_start: 0.9466 (ppp) cc_final: 0.9213 (ppp)
REVERT: A  460 MET cc_start: 0.9326 (mmm) cc_final: 0.8987 (mmm)
REVERT: B   44 MET cc_start: 0.9149 (tmm) cc_final: 0.8896 (tmm)
REVERT: B   98 MET cc_start: 0.9120 (ttm) cc_final: 0.8765 (ttm)
REVERT: B  111 MET cc_start: 0.9760 (ttp) cc_final: 0.9154 (tmm)
REVERT: B  196 MET cc_start: 0.9454 (tpt) cc_final: 0.8041 (tpp)
REVERT: B  200 MET cc_start: 0.9259 (mmm) cc_final: 0.8335 (mmm)
REVERT: B  244 MET cc_start: 0.9790 (ttm) cc_final: 0.8594 (ttt)
REVERT: B  312 MET cc_start: 0.9391 (tpp) cc_final: 0.8653 (mmm)
REVERT: B  402 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8948 (ppp)
  outliers start: 12
  outliers final: 9
  residues processed: 72
  average time/residue: 0.0825
  time to fit residues: 8.9578
Evaluate side-chains
  71 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0040
   chunk 106 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
** B 487 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 = 0.3032 r_free = 0.3032 target = 0.034028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.024141 restraints weight = 83060.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.024941 restraints weight = 54206.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.025489 restraints weight = 40704.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.025871 restraints weight = 33557.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.026155 restraints weight = 29395.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9044  Z= 0.117
  Angle     :  0.642  11.462  12223  Z= 0.311
  Chirality :  0.041   0.185   1454
  Planarity :  0.003   0.041   1547
  Dihedral  :  3.723  16.234   1249
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.79 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 20.06 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.25), residues: 1146
  helix:  2.07 (0.19), residues: 746
  sheet:  1.62 (0.63), residues: 70
  loop : -0.30 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 102 
 TYR   0.014   0.001   TYR B 163 
 PHE   0.011   0.001   PHE A 288 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9044)
  covalent geometry    : angle       0.64224 (12223)
  hydrogen bonds       : bond        0.03582 (  574)
  hydrogen bonds       : angle       4.14164 ( 1677)

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

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

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2292 Ramachandran restraints generated.
    1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.9501 (tpp) cc_final: 0.9162 (mmp)
REVERT: A   98 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8585 (tpt)
REVERT: A  111 MET cc_start: 0.8914 (tmm) cc_final: 0.8651 (tmm)
REVERT: A  196 MET cc_start: 0.9658 (tpp) cc_final: 0.9360 (tpt)
REVERT: A  223 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.9192 (mp10)
REVERT: A  276 MET cc_start: 0.8833 (ptm) cc_final: 0.8423 (ptm)
REVERT: A  312 MET cc_start: 0.9357 (mmm) cc_final: 0.8837 (tpp)
REVERT: A  402 MET cc_start: 0.9459 (ppp) cc_final: 0.9185 (ppp)
REVERT: A  460 MET cc_start: 0.9275 (mmm) cc_final: 0.8944 (mmm)
REVERT: B   98 MET cc_start: 0.9076 (ttm) cc_final: 0.8772 (ttm)
REVERT: B  111 MET cc_start: 0.9708 (ttp) cc_final: 0.9109 (tmm)
REVERT: B  159 MET cc_start: 0.9192 (tpp) cc_final: 0.8730 (tpp)
REVERT: B  196 MET cc_start: 0.9426 (tpt) cc_final: 0.8038 (tpp)
REVERT: B  200 MET cc_start: 0.9256 (mmm) cc_final: 0.8348 (mmm)
REVERT: B  244 MET cc_start: 0.9790 (ttm) cc_final: 0.8646 (ttt)
REVERT: B  312 MET cc_start: 0.9389 (tpp) cc_final: 0.8654 (mmm)
REVERT: B  402 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8915 (ppp)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0801
  time to fit residues: 8.4052
Evaluate side-chains
  70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  214 HIS
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  402 MET
Chi-restraints excluded: chain B residue  543 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 487 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 = 0.3003 r_free = 0.3003 target = 0.033000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.023731 restraints weight = 83090.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.024468 restraints weight = 53269.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.024966 restraints weight = 40128.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.025346 restraints weight = 33213.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.025611 restraints weight = 28976.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8813
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9044  Z= 0.159
  Angle     :  0.678  14.684  12223  Z= 0.329
  Chirality :  0.041   0.180   1454
  Planarity :  0.003   0.041   1547
  Dihedral  :  3.779  14.437   1249
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.14 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 20.06 %
    Favored  : 78.81 %
  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:  2.01 (0.25), residues: 1146
  helix:  2.01 (0.19), residues: 746
  sheet:  1.52 (0.63), residues: 70
  loop : -0.25 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.011   0.001   TYR A 572 
 PHE   0.011   0.001   PHE B 429 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.005   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9044)
  covalent geometry    : angle       0.67818 (12223)
  hydrogen bonds       : bond        0.03667 (  574)
  hydrogen bonds       : angle       4.30475 ( 1677)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1445.41 seconds
wall clock time: 25 minutes 40.12 seconds (1540.12 seconds total)