Starting phenix.real_space_refine
on Thu Mar 13 12:18:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsr_41599/03_2025/8tsr_41599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsr_41599/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tsr_41599/03_2025/8tsr_41599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsr_41599/03_2025/8tsr_41599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsr_41599/03_2025/8tsr_41599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsr_41599/03_2025/8tsr_41599.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.87, per 1000 atoms: 0.66
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.88
  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: 2.65

  Time building geometry restraints manager: 2.87 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: 0.04
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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.920
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.550
-------------------------------------------------------------------------------
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= 0.293
  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 : 11.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (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
 TRP   0.015   0.002   TRP A  17 
 HIS   0.015   0.002   HIS A 576 
 PHE   0.023   0.002   PHE A  56 
 TYR   0.007   0.001   TYR B 445 
 ARG   0.006   0.001   ARG A  61 

*********************** 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  : 1.083 
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: 0.2125
  time to fit residues: 50.3299
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  : 1.061 
-------------------------------------------------------------------------------
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 96 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.189994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.142188 restraints weight = 12349.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.141562 restraints weight = 15017.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.143665 restraints weight = 12474.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9018  Z= 0.244
  Angle     :  0.678  11.285  12188  Z= 0.335
  Chirality :  0.043   0.144   1452
  Planarity :  0.005   0.072   1542
  Dihedral  :  4.442  45.562   1253
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 20.39 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.25), residues: 1142
  helix:  1.54 (0.19), residues: 768
  sheet:  1.33 (0.66), residues: 66
  loop : -1.48 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.007   0.002   HIS A 576 
 PHE   0.020   0.002   PHE A 230 
 TYR   0.012   0.001   TYR A 572 
 ARG   0.006   0.001   ARG B 127 

*********************** 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
  204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 161
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7587 (mmt) cc_final: 0.7014 (mmt)
REVERT: B   14 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7800 (mtt-85)
REVERT: B   17 TRP cc_start: 0.8064 (t-100) cc_final: 0.7650 (t-100)
REVERT: B   54 ASP cc_start: 0.7585 (t0) cc_final: 0.7064 (t0)
  outliers start: 43
  outliers final: 27
  residues processed: 193
  average time/residue: 0.1933
  time to fit residues: 52.5671
Evaluate side-chains
  170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  304 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  421 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  556 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   85 SER
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  371 THR
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 109 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
** A 520 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 = 0.4299 r_free = 0.4299 target = 0.190979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.145359 restraints weight = 12463.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.143869 restraints weight = 14149.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.145810 restraints weight = 13559.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.1850

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= 0.208
  Angle     :  0.650   7.811  12188  Z= 0.323
  Chirality :  0.043   0.285   1452
  Planarity :  0.005   0.083   1542
  Dihedral  :  4.170  44.435   1250
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 22.75 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1142
  helix:  1.82 (0.19), residues: 756
  sheet:  1.40 (0.66), residues: 66
  loop : -1.31 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.004   0.001   HIS A 562 
 PHE   0.021   0.002   PHE A  56 
 TYR   0.013   0.001   TYR B 572 
 ARG   0.007   0.000   ARG A 488 

*********************** 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
  189 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 148
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7737 (mmt) cc_final: 0.7276 (mmt)
REVERT: B   54 ASP cc_start: 0.7529 (t0) cc_final: 0.6981 (t0)
  outliers start: 41
  outliers final: 30
  residues processed: 175
  average time/residue: 0.1972
  time to fit residues: 49.6465
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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  128 ILE
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  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  556 ILE
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  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain B residue  284 ILE
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  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 16 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0970
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.7560

-------------------------------------------------------------------------------
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**
B 418 GLN
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.191275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.144138 restraints weight = 12489.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142893 restraints weight = 13964.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.145236 restraints weight = 12083.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9018  Z= 0.196
  Angle     :  0.630   8.764  12188  Z= 0.309
  Chirality :  0.042   0.207   1452
  Planarity :  0.005   0.072   1542
  Dihedral  :  4.101  45.014   1250
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 23.16 %
    Favored  : 71.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.25), residues: 1142
  helix:  1.90 (0.19), residues: 756
  sheet:  1.54 (0.67), residues: 66
  loop : -1.13 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.009   0.002   HIS A 576 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.013   0.001   TYR A 439 
 ARG   0.007   0.000   ARG B 333 

*********************** 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
  198 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 144
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  200 MET cc_start: 0.6425 (mmm) cc_final: 0.5862 (mtm)
REVERT: A  242 MET cc_start: 0.7876 (mmt) cc_final: 0.7519 (mmt)
REVERT: A  517 ARG cc_start: 0.8907 (ttp-110) cc_final: 0.8589 (mtm110)
REVERT: B   54 ASP cc_start: 0.7527 (t0) cc_final: 0.6950 (t0)
REVERT: B  158 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7763 (tp)
REVERT: B  242 MET cc_start: 0.7848 (mmt) cc_final: 0.7561 (mmp)
  outliers start: 54
  outliers final: 33
  residues processed: 181
  average time/residue: 0.1820
  time to fit residues: 47.6553
Evaluate side-chains
  165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
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  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 MET
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  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  556 ILE
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  158 ILE
Chi-restraints excluded: chain B residue  159 MET
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  418 GLN
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 0 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 576 HIS
B 418 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 = 0.4288 r_free = 0.4288 target = 0.190002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.142420 restraints weight = 12357.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.142048 restraints weight = 13275.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.143811 restraints weight = 11541.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9018  Z= 0.211
  Angle     :  0.643   8.957  12188  Z= 0.315
  Chirality :  0.042   0.178   1452
  Planarity :  0.004   0.062   1542
  Dihedral  :  4.107  44.732   1250
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.87 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.25), residues: 1142
  helix:  1.84 (0.19), residues: 756
  sheet:  1.66 (0.68), residues: 66
  loop : -1.03 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  91 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.016   0.001   PHE A 230 
 TYR   0.009   0.001   TYR B 572 
 ARG   0.005   0.000   ARG B 333 

*********************** 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
  187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 135
  time to evaluate  : 1.611 
Fit side-chains
REVERT: A  108 MET cc_start: 0.8899 (tpp) cc_final: 0.8339 (ttm)
REVERT: A  242 MET cc_start: 0.7981 (mmt) cc_final: 0.7599 (mmt)
REVERT: A  301 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7691 (tt)
REVERT: A  517 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8390 (mtm110)
REVERT: B   54 ASP cc_start: 0.7527 (t0) cc_final: 0.6934 (t0)
REVERT: B  158 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7827 (tp)
REVERT: B  301 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7742 (tt)
  outliers start: 52
  outliers final: 35
  residues processed: 171
  average time/residue: 0.2248
  time to fit residues: 55.6891
Evaluate side-chains
  170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
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  186 SER
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  312 MET
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  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  556 ILE
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   35 ILE
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  158 ILE
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  304 VAL
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  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  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 16 optimal weight:    0.0670
   chunk 64 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.7920

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.190715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.142476 restraints weight = 12262.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141768 restraints weight = 13693.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.143874 restraints weight = 11795.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9018  Z= 0.201
  Angle     :  0.662  10.185  12188  Z= 0.315
  Chirality :  0.042   0.190   1452
  Planarity :  0.004   0.057   1542
  Dihedral  :  4.094  44.978   1250
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.10 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.26), residues: 1142
  helix:  1.96 (0.19), residues: 742
  sheet:  1.68 (0.70), residues: 66
  loop : -0.92 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  91 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 333 

*********************** 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
  185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.983 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.7460 (t0) cc_final: 0.6996 (t0)
REVERT: A  108 MET cc_start: 0.8845 (tpp) cc_final: 0.8443 (ttm)
REVERT: A  242 MET cc_start: 0.7973 (mmt) cc_final: 0.7631 (mmt)
REVERT: A  301 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7666 (tt)
REVERT: A  517 ARG cc_start: 0.8922 (ttp-110) cc_final: 0.8471 (mtm110)
REVERT: B   54 ASP cc_start: 0.7523 (t0) cc_final: 0.6942 (t0)
  outliers start: 48
  outliers final: 38
  residues processed: 167
  average time/residue: 0.2253
  time to fit residues: 55.3744
Evaluate side-chains
  169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 130
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  312 MET
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  556 ILE
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  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  359 LEU
Chi-restraints excluded: chain B residue  371 THR
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  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
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 68 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 107 optimal weight:    9.9990
   chunk 109 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
A 427 HIS
A 576 HIS
B 326 GLN
B 361 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.183963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.139008 restraints weight = 12519.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.136359 restraints weight = 15377.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.137981 restraints weight = 13802.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9018  Z= 0.349
  Angle     :  0.766  10.775  12188  Z= 0.376
  Chirality :  0.045   0.152   1452
  Planarity :  0.005   0.052   1542
  Dihedral  :  4.308  44.251   1250
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 25.41 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1142
  helix:  1.52 (0.19), residues: 742
  sheet:  1.52 (0.71), residues: 66
  loop : -1.00 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  91 
 HIS   0.005   0.001   HIS B 576 
 PHE   0.021   0.002   PHE A 230 
 TYR   0.025   0.002   TYR A 439 
 ARG   0.005   0.001   ARG B 333 

*********************** 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
  189 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 133
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   54 ASP cc_start: 0.7664 (t0) cc_final: 0.7127 (t0)
REVERT: A  108 MET cc_start: 0.8880 (tpp) cc_final: 0.8584 (ttm)
REVERT: A  153 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7693 (tt)
REVERT: A  242 MET cc_start: 0.8101 (mmt) cc_final: 0.7799 (mmt)
REVERT: A  402 MET cc_start: 0.7710 (ppp) cc_final: 0.7457 (ppp)
REVERT: B   43 PHE cc_start: 0.7754 (t80) cc_final: 0.7550 (t80)
REVERT: B   54 ASP cc_start: 0.7747 (t0) cc_final: 0.7056 (t0)
REVERT: B  153 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7662 (tt)
REVERT: B  242 MET cc_start: 0.7965 (mmt) cc_final: 0.7446 (mmt)
  outliers start: 56
  outliers final: 45
  residues processed: 174
  average time/residue: 0.1838
  time to fit residues: 46.2712
Evaluate side-chains
  172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 125
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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  153 ILE
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  298 LEU
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  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  556 ILE
Chi-restraints excluded: chain A residue  576 HIS
Chi-restraints excluded: chain B residue   35 ILE
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  153 ILE
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  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  359 LEU
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  474 ILE
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  571 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0570
   chunk 46 optimal weight:    0.0670
   overall best weight:    0.5836

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
A 576 HIS
B 418 GLN
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
B 468 ASN
B 576 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.190630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.138827 restraints weight = 12532.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.138582 restraints weight = 14520.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.142282 restraints weight = 9620.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2911

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= 0.180
  Angle     :  0.677  11.065  12188  Z= 0.320
  Chirality :  0.042   0.190   1452
  Planarity :  0.004   0.048   1542
  Dihedral  :  4.159  45.635   1250
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.36 %
    Favored  : 68.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.25), residues: 1142
  helix:  1.94 (0.19), residues: 742
  sheet:  1.41 (0.70), residues: 66
  loop : -0.92 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A 576 
 PHE   0.018   0.001   PHE A 115 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.011   0.000   ARG A 517 

*********************** 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
  179 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 142
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7841 (mtt180)
REVERT: A   54 ASP cc_start: 0.7521 (t0) cc_final: 0.7034 (t0)
REVERT: A  108 MET cc_start: 0.8836 (tpp) cc_final: 0.8486 (ttm)
REVERT: A  242 MET cc_start: 0.7976 (mmt) cc_final: 0.7564 (mmt)
REVERT: A  402 MET cc_start: 0.7932 (ppp) cc_final: 0.7636 (ppp)
REVERT: A  517 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8365 (mtm110)
REVERT: B   54 ASP cc_start: 0.7575 (t0) cc_final: 0.6933 (t0)
REVERT: B  418 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (mm-40)
  outliers start: 37
  outliers final: 36
  residues processed: 168
  average time/residue: 0.1853
  time to fit residues: 44.9113
Evaluate side-chains
  171 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
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  186 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  298 LEU
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  533 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  556 ILE
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  186 SER
Chi-restraints excluded: chain B residue  304 VAL
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  418 GLN
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  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
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 45 optimal weight:    8.9990
   chunk 102 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0870
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.6558

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.191200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.143147 restraints weight = 12478.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.140912 restraints weight = 16814.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.143879 restraints weight = 13422.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3023

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= 0.192
  Angle     :  0.692  12.126  12188  Z= 0.326
  Chirality :  0.042   0.191   1452
  Planarity :  0.004   0.046   1542
  Dihedral  :  4.154  45.340   1250
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 27.56 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.25), residues: 1142
  helix:  1.99 (0.19), residues: 742
  sheet:  1.29 (0.68), residues: 66
  loop : -0.92 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  91 
 HIS   0.006   0.001   HIS A 576 
 PHE   0.017   0.001   PHE A 115 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.009   0.000   ARG A 517 

*********************** 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
  181 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 137
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7471 (t0) cc_final: 0.6954 (t0)
REVERT: A  108 MET cc_start: 0.8735 (tpp) cc_final: 0.8457 (ttm)
REVERT: A  402 MET cc_start: 0.7788 (ppp) cc_final: 0.7561 (ppp)
REVERT: A  517 ARG cc_start: 0.8896 (ttp-110) cc_final: 0.8336 (mtm110)
REVERT: A  556 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (tt)
REVERT: B   54 ASP cc_start: 0.7549 (t0) cc_final: 0.6902 (t0)
  outliers start: 44
  outliers final: 35
  residues processed: 167
  average time/residue: 0.1717
  time to fit residues: 42.3600
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
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  186 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  298 LEU
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  533 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  556 ILE
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  186 SER
Chi-restraints excluded: chain B residue  304 VAL
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  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
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 107 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0570
   chunk 64 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 102 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.7698

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.190764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.143379 restraints weight = 12502.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.141208 restraints weight = 14837.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.143827 restraints weight = 12978.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.3122

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= 0.205
  Angle     :  0.713  12.840  12188  Z= 0.336
  Chirality :  0.042   0.186   1452
  Planarity :  0.004   0.044   1542
  Dihedral  :  4.162  45.209   1250
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 28.18 %
    Favored  : 67.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1142
  helix:  1.98 (0.19), residues: 742
  sheet:  1.01 (0.67), residues: 66
  loop : -0.88 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  91 
 HIS   0.006   0.001   HIS A 576 
 PHE   0.016   0.002   PHE A 115 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.008   0.000   ARG A 517 

********************** 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
  169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 1.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8069 (mtt90) cc_final: 0.7473 (ptp-110)
REVERT: A   54 ASP cc_start: 0.7492 (t0) cc_final: 0.6987 (t0)
REVERT: A  108 MET cc_start: 0.8744 (tpp) cc_final: 0.8453 (ttm)
REVERT: A  242 MET cc_start: 0.7979 (mmt) cc_final: 0.7465 (mmt)
REVERT: A  402 MET cc_start: 0.7830 (ppp) cc_final: 0.7613 (ppp)
REVERT: A  517 ARG cc_start: 0.8921 (ttp-110) cc_final: 0.8360 (mtm110)
REVERT: A  556 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7595 (tt)
REVERT: B   54 ASP cc_start: 0.7663 (t0) cc_final: 0.6989 (t0)
REVERT: B  418 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8699 (mm-40)
REVERT: B  520 GLN cc_start: 0.8249 (pt0) cc_final: 0.7945 (pt0)
  outliers start: 38
  outliers final: 35
  residues processed: 157
  average time/residue: 0.1783
  time to fit residues: 41.1307
Evaluate side-chains
  168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 131
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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  186 SER
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  298 LEU
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  533 LEU
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  556 ILE
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  304 VAL
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  418 GLN
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  533 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 113 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0980
   chunk 91 optimal weight:    6.9990
   overall best weight:    0.7582

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.190666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.144065 restraints weight = 12446.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.141610 restraints weight = 16822.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.144268 restraints weight = 13959.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.310   9018  Z= 0.394
  Angle     :  1.039  59.197  12188  Z= 0.575
  Chirality :  0.051   0.916   1452
  Planarity :  0.005   0.102   1542
  Dihedral  :  4.158  45.204   1250
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 27.56 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1142
  helix:  1.98 (0.19), residues: 742
  sheet:  0.99 (0.67), residues: 66
  loop : -0.88 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  91 
 HIS   0.149   0.007   HIS A 576 
 PHE   0.015   0.001   PHE A 115 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.007   0.000   ARG A 517 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2777.22 seconds
wall clock time: 49 minutes 31.15 seconds (2971.15 seconds total)