Starting phenix.real_space_refine
on Thu Feb 13 10:01:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tsr_41599/02_2025/8tsr_41599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tsr_41599/02_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_41599/02_2025/8tsr_41599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tsr_41599/02_2025/8tsr_41599.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tsr_41599/02_2025/8tsr_41599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tsr_41599/02_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-5592/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: 5.66, per 1000 atoms: 0.64
  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: 2.35
  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: 1.05
  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: 2.61

  Time building geometry restraints manager: 2.68 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: 0.05
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:             1.830
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     22.910
  Find NCS groups from input model:        0.280
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.400
-------------------------------------------------------------------------------
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  : 1.037 
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: 0.2114
  time to fit residues: 50.0167
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  : 1.006 
-------------------------------------------------------------------------------
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 = 0.142172 restraints weight = 12350.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.141485 restraints weight = 15072.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.143618 restraints weight = 12537.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
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  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7603 (mmt) cc_final: 0.7028 (mmt)
REVERT: B   14 ARG cc_start: 0.8071 (mtt90) cc_final: 0.7802 (mtt-85)
REVERT: B   17 TRP cc_start: 0.8063 (t-100) cc_final: 0.7650 (t-100)
REVERT: B   54 ASP cc_start: 0.7572 (t0) cc_final: 0.7056 (t0)
  outliers start: 43
  outliers final: 27
  residues processed: 193
  average time/residue: 0.2033
  time to fit residues: 55.8388
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  : 0.987 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 31 optimal weight:    0.0020
   chunk 43 optimal weight:    0.5980
   chunk 109 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0000
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0270
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.2850

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 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 = 0.4330 r_free = 0.4330 target = 0.194048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.140646 restraints weight = 12427.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.144434 restraints weight = 8311.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.146981 restraints weight = 6430.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1865

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= 0.172
  Angle     :  0.630   7.764  12188  Z= 0.310
  Chirality :  0.042   0.293   1452
  Planarity :  0.005   0.085   1542
  Dihedral  :  4.126  44.806   1250
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.85 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.96 (0.19), residues: 756
  sheet:  1.42 (0.66), residues: 66
  loop : -1.25 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 562 
 PHE   0.019   0.001   PHE A  56 
 TYR   0.013   0.001   TYR B 572 
 ARG   0.005   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
  180 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 148
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.7342 (ttm) cc_final: 0.7115 (ttm)
REVERT: A  242 MET cc_start: 0.7701 (mmt) cc_final: 0.7207 (mmt)
REVERT: B   54 ASP cc_start: 0.7465 (t0) cc_final: 0.6943 (t0)
  outliers start: 32
  outliers final: 19
  residues processed: 170
  average time/residue: 0.2033
  time to fit residues: 48.8445
Evaluate side-chains
  155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
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  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
A 418 GLN
B 418 GLN
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.190932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.144769 restraints weight = 12482.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.143799 restraints weight = 13836.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.145901 restraints weight = 12631.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9018  Z= 0.213
  Angle     :  0.641  11.560  12188  Z= 0.314
  Chirality :  0.042   0.204   1452
  Planarity :  0.005   0.071   1542
  Dihedral  :  4.083  44.612   1250
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 22.85 %
    Favored  : 72.13 %
  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:  1.62 (0.25), residues: 1142
  helix:  1.92 (0.19), residues: 756
  sheet:  1.48 (0.67), residues: 66
  loop : -1.13 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  10 
 HIS   0.011   0.002   HIS A 576 
 PHE   0.017   0.002   PHE A 230 
 TYR   0.019   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
  186 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 137
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8940 (tpp) cc_final: 0.8472 (ttm)
REVERT: A  242 MET cc_start: 0.7885 (mmt) cc_final: 0.7526 (mmt)
REVERT: A  517 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8575 (mtm110)
REVERT: B   54 ASP cc_start: 0.7526 (t0) cc_final: 0.6953 (t0)
  outliers start: 49
  outliers final: 35
  residues processed: 169
  average time/residue: 0.1842
  time to fit residues: 44.9355
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  245 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  321 ILE
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  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  284 ILE
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  418 GLN
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
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:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 39 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 107 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.5762

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

Flipped N/Q/H residues before XYZ refinement:
A 240 GLN
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 HIS
A 576 HIS
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.186395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.142879 restraints weight = 12397.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141184 restraints weight = 16205.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142340 restraints weight = 15382.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9018  Z= 0.296
  Angle     :  0.701  10.311  12188  Z= 0.347
  Chirality :  0.043   0.168   1452
  Planarity :  0.005   0.063   1542
  Dihedral  :  4.210  44.198   1250
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 23.77 %
    Favored  : 70.29 %
  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:  1.33 (0.25), residues: 1142
  helix:  1.63 (0.19), residues: 756
  sheet:  1.63 (0.69), residues: 66
  loop : -1.10 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.020   0.002   PHE A 230 
 TYR   0.022   0.002   TYR A 439 
 ARG   0.006   0.001   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
  197 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 139
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8830 (tpp) cc_final: 0.8551 (ttm)
REVERT: A  242 MET cc_start: 0.8083 (mmt) cc_final: 0.7690 (mmt)
REVERT: A  301 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7854 (tt)
REVERT: B   54 ASP cc_start: 0.7625 (t0) cc_final: 0.7037 (t0)
REVERT: B  301 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7818 (tt)
  outliers start: 58
  outliers final: 42
  residues processed: 177
  average time/residue: 0.1783
  time to fit residues: 46.0184
Evaluate side-chains
  172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 128
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   85 SER
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  186 SER
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  301 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  159 MET
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  301 LEU
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  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 64 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 83 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
A 576 HIS
B 361 ASN
B 418 GLN
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 520 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.190715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.143254 restraints weight = 12227.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.141708 restraints weight = 15940.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.145609 restraints weight = 11853.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2583

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= 0.186
  Angle     :  0.661  10.413  12188  Z= 0.311
  Chirality :  0.041   0.152   1452
  Planarity :  0.004   0.057   1542
  Dihedral  :  4.114  45.272   1250
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 25.20 %
    Favored  : 69.77 %
  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:  1.66 (0.26), residues: 1142
  helix:  1.89 (0.19), residues: 756
  sheet:  1.62 (0.70), residues: 66
  loop : -0.96 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.005   0.001   HIS A 576 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.007   0.000   ARG A 517 

*********************** 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
  187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7339 (t0) cc_final: 0.6979 (t0)
REVERT: A  242 MET cc_start: 0.7973 (mmt) cc_final: 0.7601 (mmt)
REVERT: A  301 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7700 (tt)
REVERT: A  418 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8657 (mm-40)
REVERT: A  517 ARG cc_start: 0.8916 (ttp-110) cc_final: 0.8410 (mtm110)
REVERT: B   54 ASP cc_start: 0.7563 (t0) cc_final: 0.6986 (t0)
REVERT: B  108 MET cc_start: 0.8823 (tpp) cc_final: 0.8571 (ttm)
REVERT: B  418 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8561 (mm-40)
  outliers start: 49
  outliers final: 35
  residues processed: 173
  average time/residue: 0.1975
  time to fit residues: 49.2028
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  : 0.974 
-------------------------------------------------------------------------------
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  203 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  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
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   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  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  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  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 107 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.9184

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.189610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.142867 restraints weight = 12362.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.141051 restraints weight = 15429.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.143738 restraints weight = 12804.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9018  Z= 0.214
  Angle     :  0.679  10.819  12188  Z= 0.321
  Chirality :  0.042   0.157   1452
  Planarity :  0.004   0.053   1542
  Dihedral  :  4.084  44.940   1250
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 26.23 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.68 (0.25), residues: 1142
  helix:  1.95 (0.19), residues: 742
  sheet:  1.54 (0.70), residues: 66
  loop : -0.90 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.005   0.001   HIS A 576 
 PHE   0.020   0.001   PHE A 115 
 TYR   0.020   0.001   TYR A 439 
 ARG   0.006   0.001   ARG A 127 

*********************** 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
  177 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.7359 (t0) cc_final: 0.6980 (t0)
REVERT: A  242 MET cc_start: 0.7993 (mmt) cc_final: 0.7587 (mmt)
REVERT: A  402 MET cc_start: 0.7744 (ppp) cc_final: 0.7529 (ppp)
REVERT: A  418 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8705 (mm-40)
REVERT: A  517 ARG cc_start: 0.8915 (ttp-110) cc_final: 0.8663 (mtm110)
REVERT: B   54 ASP cc_start: 0.7552 (t0) cc_final: 0.6921 (t0)
REVERT: B  153 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7558 (tt)
  outliers start: 46
  outliers final: 38
  residues processed: 166
  average time/residue: 0.1734
  time to fit residues: 42.3416
Evaluate side-chains
  169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
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  203 VAL
Chi-restraints excluded: chain A residue  275 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  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  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  153 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  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  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:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    0.3980
   chunk 0 optimal weight:    8.9990
   chunk 79 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 61 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS
B 326 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.191179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143852 restraints weight = 12563.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.142181 restraints weight = 16468.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.145567 restraints weight = 12639.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9018  Z= 0.193
  Angle     :  0.674  11.381  12188  Z= 0.317
  Chirality :  0.042   0.185   1452
  Planarity :  0.004   0.049   1542
  Dihedral  :  4.036  45.135   1250
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 26.84 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.78 (0.26), residues: 1142
  helix:  2.02 (0.19), residues: 742
  sheet:  1.45 (0.70), residues: 66
  loop : -0.84 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.018   0.001   PHE A 115 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B  14 

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

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 137
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7807 (mtt180)
REVERT: A   54 ASP cc_start: 0.7387 (t0) cc_final: 0.6923 (t0)
REVERT: A  242 MET cc_start: 0.7911 (mmt) cc_final: 0.7433 (mmt)
REVERT: A  517 ARG cc_start: 0.8909 (ttp-110) cc_final: 0.8422 (mtm110)
REVERT: B   54 ASP cc_start: 0.7545 (t0) cc_final: 0.6903 (t0)
  outliers start: 41
  outliers final: 37
  residues processed: 167
  average time/residue: 0.1729
  time to fit residues: 42.6241
Evaluate side-chains
  166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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  203 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  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  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0770
   chunk 92 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 576 HIS
** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 418 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 = 0.4308 r_free = 0.4308 target = 0.192653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143827 restraints weight = 12466.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.142029 restraints weight = 16510.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.145297 restraints weight = 12720.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9018  Z= 0.190
  Angle     :  0.685  12.152  12188  Z= 0.323
  Chirality :  0.042   0.186   1452
  Planarity :  0.004   0.046   1542
  Dihedral  :  4.085  45.142   1250
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 26.84 %
    Favored  : 68.55 %
  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:  1.81 (0.26), residues: 1142
  helix:  2.05 (0.19), residues: 746
  sheet:  1.23 (0.67), residues: 66
  loop : -0.80 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.006   0.001   HIS A 576 
 PHE   0.017   0.001   PHE A 115 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.004   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: 45
    poor density    : 136
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7785 (mtt180)
REVERT: A   54 ASP cc_start: 0.7441 (t0) cc_final: 0.6931 (t0)
REVERT: A  111 MET cc_start: 0.7346 (ttm) cc_final: 0.7124 (ttm)
REVERT: A  153 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: A  200 MET cc_start: 0.6650 (mmm) cc_final: 0.6207 (tpt)
REVERT: A  242 MET cc_start: 0.7884 (mmt) cc_final: 0.7474 (mmt)
REVERT: A  244 MET cc_start: 0.6122 (mtt) cc_final: 0.5921 (mtt)
REVERT: A  418 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8162 (mm-40)
REVERT: A  517 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8420 (mtm110)
REVERT: A  556 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7494 (tt)
REVERT: B   54 ASP cc_start: 0.7518 (t0) cc_final: 0.6876 (t0)
REVERT: B  108 MET cc_start: 0.8723 (ttm) cc_final: 0.8487 (ttm)
  outliers start: 45
  outliers final: 37
  residues processed: 168
  average time/residue: 0.1753
  time to fit residues: 43.4956
Evaluate side-chains
  170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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  153 ILE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  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  186 SER
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 110 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0000
   chunk 64 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0070
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.6002

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 576 HIS
B 240 GLN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 562 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.192929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.137954 restraints weight = 12453.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.141777 restraints weight = 8327.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.144412 restraints weight = 6477.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9018  Z= 0.191
  Angle     :  0.706  12.335  12188  Z= 0.331
  Chirality :  0.042   0.181   1452
  Planarity :  0.004   0.043   1542
  Dihedral  :  4.076  45.103   1250
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 27.36 %
    Favored  : 68.34 %
  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:  1.79 (0.26), residues: 1142
  helix:  2.04 (0.19), residues: 746
  sheet:  1.06 (0.67), residues: 66
  loop : -0.79 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  91 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.017   0.001   PHE A 115 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.004   0.000   ARG A 416 

********************** 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
  172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 130
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.7911 (mtt90) cc_final: 0.7653 (mtm-85)
REVERT: A   54 ASP cc_start: 0.7426 (t0) cc_final: 0.6966 (t0)
REVERT: A  111 MET cc_start: 0.7262 (ttm) cc_final: 0.7012 (ttm)
REVERT: A  153 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7741 (tt)
REVERT: A  196 MET cc_start: 0.4330 (tpt) cc_final: 0.3917 (tpt)
REVERT: A  242 MET cc_start: 0.7732 (mmt) cc_final: 0.7417 (mmt)
REVERT: A  418 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8486 (mm-40)
REVERT: A  517 ARG cc_start: 0.9214 (ttp-110) cc_final: 0.8577 (mtm110)
REVERT: A  556 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7542 (tt)
REVERT: B   54 ASP cc_start: 0.7504 (t0) cc_final: 0.6893 (t0)
REVERT: B  341 ASP cc_start: 0.6595 (t0) cc_final: 0.6221 (t0)
  outliers start: 42
  outliers final: 37
  residues processed: 162
  average time/residue: 0.1731
  time to fit residues: 41.5488
Evaluate side-chains
  167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
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  153 ILE
Chi-restraints excluded: chain A residue  203 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  418 GLN
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  428 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  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  186 SER
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  304 VAL
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  317 THR
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  395 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  460 MET
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 VAL
Chi-restraints excluded: chain B residue  556 ILE
Chi-restraints excluded: chain B residue  571 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9990
   chunk 113 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 ** 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 = 0.4310 r_free = 0.4310 target = 0.192711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.146334 restraints weight = 12475.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.144244 restraints weight = 15806.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.147315 restraints weight = 13292.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9018  Z= 0.197
  Angle     :  0.705  12.451  12188  Z= 0.331
  Chirality :  0.042   0.184   1452
  Planarity :  0.004   0.042   1542
  Dihedral  :  4.084  45.227   1250
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 27.36 %
    Favored  : 68.34 %
  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:  1.80 (0.25), residues: 1142
  helix:  2.04 (0.19), residues: 746
  sheet:  0.90 (0.67), residues: 66
  loop : -0.74 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  91 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.016   0.001   PHE A 115 
 TYR   0.019   0.001   TYR A 439 
 ARG   0.005   0.000   ARG A 416 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2747.73 seconds
wall clock time: 50 minutes 12.05 seconds (3012.05 seconds total)