Starting phenix.real_space_refine
on Sat Aug 23 01:06:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsr_41599/08_2025/8tsr_41599.map"
  }
  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=   0.002 sd=   0.038
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    5630      2.51       5
     N    1548      2.21       5
     O    1656      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8888
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4444
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 13, 'TRANS': 559}
    Chain: "B"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4444
          Classifications: {'peptide': 573}
          Link IDs: {'PTRANS': 13, 'TRANS': 559}
  Time building chain proxies: 2.37, per 1000 atoms: 0.27
  Number of scatterers: 8888
  At special positions: 0
  Unit cell: (67.095, 139.515, 135.255, 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    1656      8.00
     N    1548      7.00
     C    5630      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: 0.90
  Conformation dependent library (CDL) restraints added in 375.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      71.2% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  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: 3.855A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
      removed outlier: 3.812A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 66
      removed outlier: 4.016A  pdb=" N   LEU A  64 " --> pdb=" O   ASP A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 109
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 113 through 119
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 3.515A  pdb=" N   LEU A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   SER A 132 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 201
      removed outlier: 4.378A  pdb=" N   ILE A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 4.443A  pdb=" N   GLY A 201 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 211
      removed outlier: 3.590A  pdb=" N   ALA A 207 " --> pdb=" O   VAL A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 272
      removed outlier: 4.434A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 280 through 294
    Processing helix  chain 'A' and resid 294 through 323
      removed outlier: 3.747A  pdb=" N   LEU A 298 " --> pdb=" O   LEU A 294 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.099A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 410
      No H-bonds generated for 'chain 'A' and resid 408 through 410'
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 433 through 438
      removed outlier: 3.731A  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 460 through 465
      removed outlier: 3.687A  pdb=" N   LYS A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 471
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 512 through 526
    Processing helix  chain 'A' and resid 538 through 544
      removed outlier: 3.698A  pdb=" N   ILE A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 569
    Processing helix  chain 'A' and resid 570 through 579
    Processing helix  chain 'B' and resid 8 through 21
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 47
      removed outlier: 3.854A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.671A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU B  52 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 66 through 109
    Processing helix  chain 'B' and resid 113 through 119
    Processing helix  chain 'B' and resid 120 through 164
      removed outlier: 3.977A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 200
      removed outlier: 4.445A  pdb=" N   ILE B 170 " --> pdb=" O   GLN B 166 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 203 through 211
      removed outlier: 3.681A  pdb=" N   ALA B 207 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 4.529A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 275 through 279
      removed outlier: 4.024A  pdb=" N   SER B 278 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B 279 " --> pdb=" O   MET B 276 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 275 through 279'
    Processing helix  chain 'B' and resid 280 through 294
    Processing helix  chain 'B' and resid 294 through 323
      removed outlier: 3.742A  pdb=" N   LEU B 298 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.118A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 410
      No H-bonds generated for 'chain 'B' and resid 408 through 410'
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 433 through 438
      removed outlier: 3.858A  pdb=" N   ALA B 438 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 460 through 465
      removed outlier: 3.813A  pdb=" N   LYS B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 512 through 526
    Processing helix  chain 'B' and resid 538 through 544
      removed outlier: 3.844A  pdb=" N   ILE B 542 " --> pdb=" O   ARG B 538 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 6.637A  pdb=" N   ARG A 360 " --> pdb=" O   THR A 348 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   THR A 348 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 5.720A  pdb=" N   PHE A 344 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   LEU A 401 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   ASN A 346 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.925A  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 423
      removed outlier: 6.376A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLU A 558 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 431 through 432
    Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 366
      removed outlier: 6.738A  pdb=" N   ARG B 360 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   THR B 348 " --> pdb=" O   ARG B 360 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   ILE B 362 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 423
      removed outlier: 6.295A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 431 through 432

    595 hydrogen bonds defined for protein.
    1755 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: 1.56

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2296
        1.33 -     1.45: 1521
        1.45 -     1.57: 5097
        1.57 -     1.69: 0
        1.69 -     1.81: 104
  Bond restraints: 9018
  Sorted by residual:
  bond pdb=" N   VAL B 555 "
       pdb=" CA  VAL B 555 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.19e-02 7.06e+03 9.27e+00
  bond pdb=" N   ILE B 556 "
       pdb=" CA  ILE B 556 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.83e+00
  bond pdb=" N   ILE A 556 "
       pdb=" CA  ILE A 556 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.30e-02 5.92e+03 8.54e+00
  bond pdb=" N   VAL B 549 "
       pdb=" CA  VAL B 549 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.17e-02 7.31e+03 8.49e+00
  bond pdb=" N   VAL A 422 "
       pdb=" CA  VAL A 422 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.35e+00
  ... (remaining 9013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 11745
        1.99 -     3.99: 373
        3.99 -     5.98: 42
        5.98 -     7.97: 21
        7.97 -     9.96: 7
  Bond angle restraints: 12188
  Sorted by residual:
  angle pdb=" CA  ILE A 556 "
        pdb=" C   ILE A 556 "
        pdb=" O   ILE A 556 "
      ideal   model   delta    sigma   weight residual
     121.58  118.23    3.35 1.00e+00 1.00e+00 1.12e+01
  angle pdb=" CB  MET A 291 "
        pdb=" CG  MET A 291 "
        pdb=" SD  MET A 291 "
      ideal   model   delta    sigma   weight residual
     112.70  122.66   -9.96 3.00e+00 1.11e-01 1.10e+01
  angle pdb=" CB  MET B 291 "
        pdb=" CG  MET B 291 "
        pdb=" SD  MET B 291 "
      ideal   model   delta    sigma   weight residual
     112.70  122.63   -9.93 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CA  GLU A 552 "
        pdb=" C   GLU A 552 "
        pdb=" O   GLU A 552 "
      ideal   model   delta    sigma   weight residual
     121.89  118.02    3.87 1.17e+00 7.31e-01 1.09e+01
  angle pdb=" CA  VAL A 113 "
        pdb=" C   VAL A 113 "
        pdb=" O   VAL A 113 "
      ideal   model   delta    sigma   weight residual
     121.05  117.71    3.34 1.04e+00 9.25e-01 1.03e+01
  ... (remaining 12183 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4739
       17.56 -    35.12: 613
       35.12 -    52.68: 106
       52.68 -    70.24: 29
       70.24 -    87.80: 5
  Dihedral angle restraints: 5492
    sinusoidal: 2178
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  ARG A 360 "
           pdb=" C   ARG A 360 "
           pdb=" N   ASN A 361 "
           pdb=" CA  ASN A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.15   20.85     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ASP B 471 "
           pdb=" CB  ASP B 471 "
           pdb=" CG  ASP B 471 "
           pdb=" OD1 ASP B 471 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.35   56.35     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CA  ASP A 471 "
           pdb=" CB  ASP A 471 "
           pdb=" CG  ASP A 471 "
           pdb=" OD1 ASP A 471 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.50   55.50     1      2.00e+01 2.50e-03 1.04e+01
  ... (remaining 5489 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1071
       0.048 -    0.096: 296
       0.096 -    0.144: 60
       0.144 -    0.192: 21
       0.192 -    0.240: 4
  Chirality restraints: 1452
  Sorted by residual:
  chirality pdb=" CA  ILE A 556 "
            pdb=" N   ILE A 556 "
            pdb=" C   ILE A 556 "
            pdb=" CB  ILE A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  ILE B  20 "
            pdb=" N   ILE B  20 "
            pdb=" C   ILE B  20 "
            pdb=" CB  ILE B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  VAL A 422 "
            pdb=" N   VAL A 422 "
            pdb=" C   VAL A 422 "
            pdb=" CB  VAL A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.53e-01
  ... (remaining 1449 not shown)

  Planarity restraints: 1542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 499 "    0.074 5.00e-02 4.00e+02   1.10e-01 1.94e+01
        pdb=" N   PRO B 500 "   -0.190 5.00e-02 4.00e+02
        pdb=" CA  PRO B 500 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B 500 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 499 "   -0.072 5.00e-02 4.00e+02   1.08e-01 1.87e+01
        pdb=" N   PRO A 500 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  21 "   -0.040 5.00e-02 4.00e+02   6.03e-02 5.83e+00
        pdb=" N   PRO A  22 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  22 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  22 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1539 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1257
        2.76 -     3.29: 9334
        3.29 -     3.83: 15139
        3.83 -     4.36: 16444
        4.36 -     4.90: 27982
  Nonbonded interactions: 70156
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 117 "
            pdb=" OH  TYR B 393 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG  SER A 249 "
            pdb=" OG  SER B  86 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OD2 ASP A 117 "
            pdb=" OH  TYR A 393 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OE2 GLU B 506 "
            pdb=" OG1 THR B 541 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG1 THR B 350 "
            pdb=" OD2 ASP B 396 "
     model   vdw
     2.276 3.040
  ... (remaining 70151 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.260
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   9018  Z= 0.286
  Angle     :  0.832   9.963  12188  Z= 0.483
  Chirality :  0.049   0.240   1452
  Planarity :  0.007   0.110   1542
  Dihedral  : 16.020  87.802   3348
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 23.26 %
    Favored  : 76.23 %
  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 aren not related in a simple way.
  whole:  0.80 (0.25), residues: 1142
  helix:  1.57 (0.19), residues: 722
  sheet:  1.12 (0.65), residues: 66
  loop : -1.84 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  61 
 TYR   0.007   0.001   TYR B 445 
 PHE   0.023   0.002   PHE A  56 
 TRP   0.015   0.002   TRP A  17 
 HIS   0.015   0.002   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 9018)
  covalent geometry    : angle       0.83151 (12188)
  hydrogen bonds       : bond        0.13745 (  595)
  hydrogen bonds       : angle       5.31200 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 167
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 ASP cc_start: 0.7222 (t0) cc_final: 0.6977 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 170
  average time/residue: 0.1009
  time to fit residues: 23.7504
Evaluate side-chains
  140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  556 ILE
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.192346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.142469 restraints weight = 12499.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.141458 restraints weight = 16643.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.145695 restraints weight = 10977.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145088 restraints weight = 7008.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.145496 restraints weight = 7334.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9018  Z= 0.143
  Angle     :  0.651  11.488  12188  Z= 0.319
  Chirality :  0.042   0.143   1452
  Planarity :  0.005   0.071   1542
  Dihedral  :  4.389  46.065   1253
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.00 %
    Favored  : 75.41 %
  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 aren not related in a simple way.
  whole:  1.24 (0.26), residues: 1142
  helix:  1.66 (0.19), residues: 768
  sheet:  1.36 (0.66), residues: 66
  loop : -1.48 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 127 
 TYR   0.012   0.001   TYR A 572 
 PHE   0.017   0.002   PHE A 230 
 TRP   0.008   0.001   TRP B  17 
 HIS   0.007   0.002   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9018)
  covalent geometry    : angle       0.65064 (12188)
  hydrogen bonds       : bond        0.05300 (  595)
  hydrogen bonds       : angle       4.46299 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 165
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7538 (mmt) cc_final: 0.7033 (mmt)
REVERT: B   14 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7787 (mtt-85)
REVERT: B   17 TRP cc_start: 0.8014 (t-100) cc_final: 0.7607 (t-100)
REVERT: B   54 ASP cc_start: 0.7506 (t0) cc_final: 0.7014 (t0)
  outliers start: 35
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0873
  time to fit residues: 23.5739
Evaluate side-chains
  162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 52 optimal weight:    0.0010
   chunk 74 optimal weight:    0.0980
   chunk 50 optimal weight:    0.0270
   chunk 28 optimal weight:    0.7980
   chunk 77 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.1980
   chunk 34 optimal weight:    9.9990
   chunk 57 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 113 optimal weight:    8.9990
   overall best weight:    0.2244

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 GLN
** B 520 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 = 0.4347 r_free = 0.4347 target = 0.196283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.146228 restraints weight = 12403.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.147238 restraints weight = 12484.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.150683 restraints weight = 8102.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.150747 restraints weight = 5910.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.150842 restraints weight = 5859.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   9018  Z= 0.124
  Angle     :  0.611   7.859  12188  Z= 0.299
  Chirality :  0.041   0.190   1452
  Planarity :  0.004   0.059   1542
  Dihedral  :  4.015  44.459   1248
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.03 %
    Favored  : 74.69 %
  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 aren not related in a simple way.
  whole:  1.67 (0.26), residues: 1142
  helix:  2.00 (0.19), residues: 756
  sheet:  1.56 (0.66), residues: 66
  loop : -1.22 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 517 
 TYR   0.012   0.001   TYR B 572 
 PHE   0.016   0.001   PHE A 189 
 TRP   0.007   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9018)
  covalent geometry    : angle       0.61137 (12188)
  hydrogen bonds       : bond        0.04596 (  595)
  hydrogen bonds       : angle       4.20162 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7195 (ttm) cc_final: 0.6971 (ttm)
REVERT: A  242 MET cc_start: 0.7764 (mmt) cc_final: 0.7379 (mmt)
REVERT: A  418 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8492 (mm-40)
REVERT: B   14 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7791 (mtt-85)
REVERT: B   54 ASP cc_start: 0.7517 (t0) cc_final: 0.6990 (t0)
REVERT: B  196 MET cc_start: 0.4075 (tpt) cc_final: 0.3116 (tpt)
  outliers start: 32
  outliers final: 18
  residues processed: 181
  average time/residue: 0.0876
  time to fit residues: 22.5715
Evaluate side-chains
  155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  488 ARG
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0000
   chunk 87 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 91 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
A 418 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 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 = 0.4305 r_free = 0.4305 target = 0.191759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.145887 restraints weight = 12577.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.143812 restraints weight = 16564.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.146531 restraints weight = 13867.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.146825 restraints weight = 9353.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147346 restraints weight = 9142.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9018  Z= 0.143
  Angle     :  0.634   9.035  12188  Z= 0.312
  Chirality :  0.042   0.250   1452
  Planarity :  0.004   0.060   1542
  Dihedral  :  3.993  44.514   1248
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 22.85 %
    Favored  : 72.23 %
  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 aren not related in a simple way.
  whole:  1.68 (0.26), residues: 1142
  helix:  1.98 (0.19), residues: 756
  sheet:  1.63 (0.67), residues: 66
  loop : -1.14 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 127 
 TYR   0.015   0.001   TYR B 439 
 PHE   0.018   0.002   PHE A 230 
 TRP   0.005   0.001   TRP A  10 
 HIS   0.012   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9018)
  covalent geometry    : angle       0.63369 (12188)
  hydrogen bonds       : bond        0.04887 (  595)
  hydrogen bonds       : angle       4.23294 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7771 (mmt) cc_final: 0.7466 (mmt)
REVERT: A  418 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8632 (mm-40)
REVERT: B   54 ASP cc_start: 0.7554 (t0) cc_final: 0.6989 (t0)
  outliers start: 48
  outliers final: 32
  residues processed: 170
  average time/residue: 0.0860
  time to fit residues: 21.1965
Evaluate side-chains
  163 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0570
   chunk 111 optimal weight:    0.0050
   chunk 96 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 60 optimal weight:    0.5980
   chunk 32 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.4912

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 576 HIS
B 418 GLN
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.193780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.142452 restraints weight = 12428.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.143936 restraints weight = 9201.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144161 restraints weight = 7559.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.144911 restraints weight = 7489.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.144984 restraints weight = 6843.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9018  Z= 0.128
  Angle     :  0.627   9.452  12188  Z= 0.306
  Chirality :  0.041   0.218   1452
  Planarity :  0.005   0.095   1542
  Dihedral  :  3.987  45.001   1248
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.39 %
    Favored  : 71.52 %
  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 aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1142
  helix:  2.08 (0.19), residues: 754
  sheet:  1.61 (0.67), residues: 66
  loop : -1.13 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 488 
 TYR   0.012   0.001   TYR A 439 
 PHE   0.014   0.001   PHE A 189 
 TRP   0.005   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 9018)
  covalent geometry    : angle       0.62740 (12188)
  hydrogen bonds       : bond        0.04633 (  595)
  hydrogen bonds       : angle       4.12416 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 144
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7863 (mmt) cc_final: 0.7531 (mmt)
REVERT: A  402 MET cc_start: 0.8129 (ppp) cc_final: 0.7876 (ppp)
REVERT: A  418 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8757 (mm-40)
REVERT: B   54 ASP cc_start: 0.7510 (t0) cc_final: 0.6949 (t0)
REVERT: B  402 MET cc_start: 0.8294 (ppp) cc_final: 0.8006 (ppp)
  outliers start: 40
  outliers final: 26
  residues processed: 171
  average time/residue: 0.0908
  time to fit residues: 21.9996
Evaluate side-chains
  156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  244 MET
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 113 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 46 optimal weight:    0.0980
   chunk 90 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 576 HIS
B 520 GLN
B 576 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.193291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.137979 restraints weight = 12477.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.142018 restraints weight = 8254.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.144558 restraints weight = 6394.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.146312 restraints weight = 5469.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.147078 restraints weight = 4962.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9018  Z= 0.133
  Angle     :  0.655  10.855  12188  Z= 0.313
  Chirality :  0.041   0.208   1452
  Planarity :  0.005   0.083   1542
  Dihedral  :  3.989  44.812   1248
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 24.49 %
    Favored  : 70.90 %
  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 aren not related in a simple way.
  whole:  1.87 (0.26), residues: 1142
  helix:  2.16 (0.19), residues: 742
  sheet:  1.56 (0.67), residues: 66
  loop : -1.00 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 517 
 TYR   0.019   0.001   TYR A 439 
 PHE   0.021   0.001   PHE B  13 
 TRP   0.005   0.001   TRP B  91 
 HIS   0.007   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9018)
  covalent geometry    : angle       0.65515 (12188)
  hydrogen bonds       : bond        0.04620 (  595)
  hydrogen bonds       : angle       4.10981 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7407 (t0) cc_final: 0.7029 (t0)
REVERT: A   75 MET cc_start: 0.6464 (tmm) cc_final: 0.6229 (tmm)
REVERT: A  242 MET cc_start: 0.7845 (mmt) cc_final: 0.7520 (mmt)
REVERT: A  405 HIS cc_start: 0.6187 (m170) cc_final: 0.5734 (m170)
REVERT: A  418 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8457 (mm-40)
REVERT: A  517 ARG cc_start: 0.9129 (ttp-110) cc_final: 0.8745 (mtm110)
REVERT: B   54 ASP cc_start: 0.7529 (t0) cc_final: 0.6994 (t0)
REVERT: B  242 MET cc_start: 0.7944 (mmt) cc_final: 0.7584 (mmp)
  outliers start: 45
  outliers final: 35
  residues processed: 164
  average time/residue: 0.0861
  time to fit residues: 20.3477
Evaluate side-chains
  168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS
A 418 GLN
A 576 HIS
B 240 GLN
B 576 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.191841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140997 restraints weight = 12508.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.140399 restraints weight = 15440.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.144322 restraints weight = 11618.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144113 restraints weight = 8138.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.144852 restraints weight = 7740.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9018  Z= 0.142
  Angle     :  0.672  10.183  12188  Z= 0.320
  Chirality :  0.042   0.176   1452
  Planarity :  0.005   0.071   1542
  Dihedral  :  4.010  44.900   1248
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.67 %
    Favored  : 71.41 %
  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 aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1142
  helix:  2.09 (0.19), residues: 742
  sheet:  1.64 (0.68), residues: 66
  loop : -0.99 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  14 
 TYR   0.020   0.001   TYR A 439 
 PHE   0.017   0.002   PHE A 115 
 TRP   0.006   0.001   TRP B  91 
 HIS   0.003   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9018)
  covalent geometry    : angle       0.67174 (12188)
  hydrogen bonds       : bond        0.04743 (  595)
  hydrogen bonds       : angle       4.14799 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 131
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7484 (t0) cc_final: 0.7036 (t0)
REVERT: A  242 MET cc_start: 0.7826 (mmt) cc_final: 0.7521 (mmt)
REVERT: A  418 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8406 (mm-40)
REVERT: A  517 ARG cc_start: 0.8970 (ttp-110) cc_final: 0.8682 (mtm110)
REVERT: B   54 ASP cc_start: 0.7559 (t0) cc_final: 0.6977 (t0)
  outliers start: 48
  outliers final: 41
  residues processed: 163
  average time/residue: 0.0764
  time to fit residues: 18.4365
Evaluate side-chains
  169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 127
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   chunk 46 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 576 HIS
B 576 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.192413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.141976 restraints weight = 12422.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.141910 restraints weight = 13620.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.144964 restraints weight = 10033.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.144761 restraints weight = 7280.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.145082 restraints weight = 6850.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9018  Z= 0.134
  Angle     :  0.677  11.498  12188  Z= 0.320
  Chirality :  0.041   0.160   1452
  Planarity :  0.004   0.061   1542
  Dihedral  :  3.998  45.176   1248
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 23.98 %
    Favored  : 71.21 %
  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 aren not related in a simple way.
  whole:  1.82 (0.25), residues: 1142
  helix:  2.09 (0.19), residues: 742
  sheet:  1.62 (0.68), residues: 66
  loop : -0.96 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  14 
 TYR   0.019   0.001   TYR A 439 
 PHE   0.025   0.002   PHE B 115 
 TRP   0.007   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9018)
  covalent geometry    : angle       0.67692 (12188)
  hydrogen bonds       : bond        0.04651 (  595)
  hydrogen bonds       : angle       4.11804 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 131
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7452 (t0) cc_final: 0.6950 (t0)
REVERT: A  242 MET cc_start: 0.7794 (mmt) cc_final: 0.7509 (mmt)
REVERT: A  517 ARG cc_start: 0.8961 (ttp-110) cc_final: 0.8421 (mtm110)
REVERT: B   54 ASP cc_start: 0.7572 (t0) cc_final: 0.6959 (t0)
  outliers start: 47
  outliers final: 39
  residues processed: 163
  average time/residue: 0.0806
  time to fit residues: 19.2959
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 104 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0670
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.9724

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
A 576 HIS
B 576 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.190806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.142924 restraints weight = 12370.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.144032 restraints weight = 12440.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.145278 restraints weight = 11040.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145553 restraints weight = 8361.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.145788 restraints weight = 7802.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9018  Z= 0.150
  Angle     :  0.700  11.838  12188  Z= 0.333
  Chirality :  0.042   0.186   1452
  Planarity :  0.004   0.057   1542
  Dihedral  :  4.036  45.087   1248
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 24.49 %
    Favored  : 71.21 %
  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 aren not related in a simple way.
  whole:  1.73 (0.25), residues: 1142
  helix:  2.00 (0.19), residues: 742
  sheet:  1.53 (0.68), residues: 66
  loop : -0.92 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  14 
 TYR   0.021   0.001   TYR A 439 
 PHE   0.025   0.002   PHE B 115 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9018)
  covalent geometry    : angle       0.69991 (12188)
  hydrogen bonds       : bond        0.04855 (  595)
  hydrogen bonds       : angle       4.18812 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7505 (t0) cc_final: 0.7022 (t0)
REVERT: A  242 MET cc_start: 0.7908 (mmt) cc_final: 0.7545 (mmt)
REVERT: A  244 MET cc_start: 0.7071 (mmm) cc_final: 0.6797 (mmm)
REVERT: A  517 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8374 (mtm110)
REVERT: B   54 ASP cc_start: 0.7579 (t0) cc_final: 0.6909 (t0)
REVERT: B  242 MET cc_start: 0.7870 (mmt) cc_final: 0.7460 (mmt)
  outliers start: 42
  outliers final: 42
  residues processed: 160
  average time/residue: 0.0734
  time to fit residues: 17.7275
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   chunk 102 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 0 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
B 527 GLN
B 576 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.192822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.144110 restraints weight = 12408.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.143548 restraints weight = 14881.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.147347 restraints weight = 10939.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.146758 restraints weight = 8195.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.147360 restraints weight = 7038.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.3009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9018  Z= 0.132
  Angle     :  0.698  12.694  12188  Z= 0.330
  Chirality :  0.042   0.191   1452
  Planarity :  0.004   0.052   1542
  Dihedral  :  4.011  45.583   1248
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.90 %
    Favored  : 71.00 %
  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 aren not related in a simple way.
  whole:  1.83 (0.26), residues: 1142
  helix:  2.08 (0.19), residues: 742
  sheet:  1.45 (0.67), residues: 66
  loop : -0.86 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  14 
 TYR   0.019   0.001   TYR A 439 
 PHE   0.026   0.002   PHE B 115 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9018)
  covalent geometry    : angle       0.69769 (12188)
  hydrogen bonds       : bond        0.04666 (  595)
  hydrogen bonds       : angle       4.12608 ( 1755)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7368 (ptp-110)
REVERT: A   54 ASP cc_start: 0.7442 (t0) cc_final: 0.6990 (t0)
REVERT: A  242 MET cc_start: 0.7812 (mmt) cc_final: 0.7436 (mmt)
REVERT: A  244 MET cc_start: 0.7123 (mmm) cc_final: 0.6884 (mmm)
REVERT: A  517 ARG cc_start: 0.8938 (ttp-110) cc_final: 0.8433 (mtm110)
REVERT: B   54 ASP cc_start: 0.7571 (t0) cc_final: 0.6939 (t0)
REVERT: B  402 MET cc_start: 0.7654 (ppp) cc_final: 0.7430 (ppp)
REVERT: B  513 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7806 (p)
  outliers start: 40
  outliers final: 36
  residues processed: 154
  average time/residue: 0.0780
  time to fit residues: 17.9922
Evaluate side-chains
  164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  576 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 71 optimal weight:    0.4980
   chunk 76 optimal weight:    1.9990
   chunk 102 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0670
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.193165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.143337 restraints weight = 12287.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.142456 restraints weight = 14985.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.145460 restraints weight = 10797.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.146054 restraints weight = 7734.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.146681 restraints weight = 8290.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9018  Z= 0.130
  Angle     :  0.692  12.331  12188  Z= 0.327
  Chirality :  0.042   0.197   1452
  Planarity :  0.004   0.048   1542
  Dihedral  :  4.009  45.464   1248
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 25.41 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.25), residues: 1142
  helix:  2.12 (0.19), residues: 742
  sheet:  1.30 (0.67), residues: 66
  loop : -0.84 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  14 
 TYR   0.018   0.001   TYR A 439 
 PHE   0.026   0.001   PHE B 115 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9018)
  covalent geometry    : angle       0.69187 (12188)
  hydrogen bonds       : bond        0.04583 (  595)
  hydrogen bonds       : angle       4.08837 ( 1755)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1586.33 seconds
wall clock time: 28 minutes 8.93 seconds (1688.93 seconds total)