Starting phenix.real_space_refine
on Tue Mar 11 19:15:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7met_23803/03_2025/7met_23803.cif"
  }
  resolution = 3.97
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      2      4.86       5
     C    4121      2.51       5
     N    1169      2.21       5
     O    1209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6521
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 564, 3643
          Classifications: {'peptide': 564}
          Incomplete info: {'truncation_to_alanine': 222}
          Link IDs: {'PTRANS': 13, 'TRANS': 550}
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 799
          Unresolved non-hydrogen angles: 1029
          Unresolved non-hydrogen dihedrals: 635
          Unresolved non-hydrogen chiralities: 78
          Planarities with less than four sites: {'GLN:plan1': 22, 'ARG:plan': 16, 'TYR:plan': 9, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 7, 'GLU:plan': 15, 'ASP:plan': 19}
          Unresolved non-hydrogen planarities: 477
    Chain: "B"
      Number of atoms: 2834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 2834
          Classifications: {'peptide': 455}
          Incomplete info: {'truncation_to_alanine': 211}
          Link IDs: {'PTRANS': 10, 'TRANS': 444}
          Chain breaks: 1
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 756
          Unresolved non-hydrogen angles: 972
          Unresolved non-hydrogen dihedrals: 597
          Unresolved non-hydrogen chiralities: 76
          Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 8, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 18, 'PHE:plan': 7, 'GLU:plan': 15, 'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 448
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 44
          Unusual residues: {'Z5G': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.28, per 1000 atoms: 0.66
  Number of scatterers: 6521
  At special positions: 0
  Unit cell: (80.56, 81.62, 136.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      20     16.00
     O    1209      8.00
     N    1169      7.00
     C    4121      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1902

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      68.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 16
      removed outlier: 3.733A  pdb=" N   SER A  13 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR A  14 " --> pdb=" O   ARG A  10 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU A  15 " --> pdb=" O   LEU A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 52
      removed outlier: 3.664A  pdb=" N   LEU A  23 " --> pdb=" O   TRP A  19 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LEU A  24 " --> pdb=" O   GLY A  20 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A  25 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A  26 " --> pdb=" O   ALA A  22 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A  27 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   GLY A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   PHE A  29 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ALA A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS A  41 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 103
      Proline residue:  A  62  - end of helix
      removed outlier: 4.334A  pdb=" N   LEU A 103 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 114
      removed outlier: 3.825A  pdb=" N   TYR A 110 " --> pdb=" O   PRO A 106 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN A 113 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 158
    Processing helix  chain 'A' and resid 167 through 207
      removed outlier: 4.201A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN A 189 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 214
    Processing helix  chain 'A' and resid 216 through 265
      removed outlier: 4.471A  pdb=" N   GLU A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   SER A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      Proline residue:  A 247  - end of helix
      removed outlier: 3.630A  pdb=" N   LEU A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 274
      removed outlier: 3.921A  pdb=" N   THR A 273 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   THR A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 269 through 274'
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 288 through 309
      removed outlier: 4.274A  pdb=" N   ASN A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   GLU A 300 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS A 301 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 315
      removed outlier: 3.961A  pdb=" N   LEU A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 380
      removed outlier: 4.040A  pdb=" N   SER A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 402
    Processing helix  chain 'A' and resid 403 through 410
    Processing helix  chain 'A' and resid 424 through 429
      removed outlier: 3.508A  pdb=" N   ILE A 429 " --> pdb=" O   VAL A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 448 through 450
      No H-bonds generated for 'chain 'A' and resid 448 through 450'
    Processing helix  chain 'A' and resid 451 through 458
      removed outlier: 3.801A  pdb=" N   LEU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.915A  pdb=" N   SER A 474 " --> pdb=" O   GLY A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 490
    Processing helix  chain 'A' and resid 507 through 522
      removed outlier: 3.687A  pdb=" N   GLN A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP A 521 " --> pdb=" O   GLU A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 537
    Processing helix  chain 'A' and resid 554 through 560
    Processing helix  chain 'A' and resid 560 through 570
    Processing helix  chain 'B' and resid 8 through 16
      removed outlier: 3.786A  pdb=" N   ILE B  12 " --> pdb=" O   TYR B   8 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   SER B  13 " --> pdb=" O   LEU B   9 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   TYR B  14 " --> pdb=" O   ARG B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 53
      removed outlier: 3.692A  pdb=" N   LEU B  23 " --> pdb=" O   TRP B  19 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   LEU B  24 " --> pdb=" O   GLY B  20 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   VAL B  25 " --> pdb=" O   VAL B  21 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LEU B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE B  27 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   ALA B  40 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS B  41 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B  47 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 105
      Proline residue:  B  62  - end of helix
      removed outlier: 3.677A  pdb=" N   ARG B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 113
      removed outlier: 3.832A  pdb=" N   LEU B 111 " --> pdb=" O   ALA B 107 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASP B 112 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 158
      removed outlier: 3.623A  pdb=" N   MET B 123 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   VAL B 126 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR B 157 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 287
    Processing helix  chain 'B' and resid 288 through 296
    Processing helix  chain 'B' and resid 297 through 316
      removed outlier: 3.770A  pdb=" N   LYS B 301 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ALA B 308 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   HIS B 310 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   SER B 311 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL B 312 " --> pdb=" O   ALA B 308 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU B 315 " --> pdb=" O   SER B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 347
      No H-bonds generated for 'chain 'B' and resid 345 through 347'
    Processing helix  chain 'B' and resid 374 through 382
      removed outlier: 4.037A  pdb=" N   LEU B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 410
    Processing helix  chain 'B' and resid 424 through 430
      removed outlier: 3.720A  pdb=" N   ALA B 430 " --> pdb=" O   ARG B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 449
    Processing helix  chain 'B' and resid 451 through 458
      removed outlier: 4.280A  pdb=" N   LEU B 458 " --> pdb=" O   PHE B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 490
      removed outlier: 3.826A  pdb=" N   ASN B 490 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 520
    Processing helix  chain 'B' and resid 530 through 537
    Processing helix  chain 'B' and resid 553 through 561
      removed outlier: 3.761A  pdb=" N   LEU B 557 " --> pdb=" O   THR B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 570
      removed outlier: 3.804A  pdb=" N   TYR B 565 " --> pdb=" O   HIS B 561 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLN B 566 " --> pdb=" O   GLY B 562 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 343
      removed outlier: 7.605A  pdb=" N   LEU A 342 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   LYS A 352 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 367
      removed outlier: 3.598A  pdb=" N   VAL A 367 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE A 540 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLY A 552 " --> pdb=" O   ILE A 540 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 413
    Processing sheet with id=AA4, first strand: chain 'B' and resid 335 through 338
      removed outlier: 3.621A  pdb=" N   ILE B 335 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 342 through 344
      removed outlier: 6.744A  pdb=" N   LEU B 342 " --> pdb=" O   ALA B 350 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR B 348 " --> pdb=" O   TYR B 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 414
      removed outlier: 3.580A  pdb=" N   ILE B 495 " --> pdb=" O   ALA B 412 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   ALA B 365 " --> pdb=" O   VAL B 541 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   MET B 543 " --> pdb=" O   ALA B 365 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   VAL B 367 " --> pdb=" O   MET B 543 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   VAL B 542 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1413 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: 2.05

  Time building geometry restraints manager: 2.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1129
        1.32 -     1.44: 1588
        1.44 -     1.56: 3840
        1.56 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 6596
  Sorted by residual:
  bond pdb=" C08 Z5G A 601 "
       pdb=" N10 Z5G A 601 "
    ideal  model  delta    sigma   weight residual
    1.345  1.456 -0.111 2.00e-02 2.50e+03 3.07e+01
  bond pdb=" C08 Z5G A 602 "
       pdb=" N10 Z5G A 602 "
    ideal  model  delta    sigma   weight residual
    1.345  1.454 -0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C11 Z5G A 601 "
       pdb=" N10 Z5G A 601 "
    ideal  model  delta    sigma   weight residual
    1.375  1.454 -0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" C11 Z5G A 602 "
       pdb=" N10 Z5G A 602 "
    ideal  model  delta    sigma   weight residual
    1.375  1.448 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" C02 Z5G A 601 "
       pdb="CL01 Z5G A 601 "
    ideal  model  delta    sigma   weight residual
    1.729  1.786 -0.057 2.00e-02 2.50e+03 8.05e+00
  ... (remaining 6591 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 8830
        1.69 -     3.37: 135
        3.37 -     5.06: 49
        5.06 -     6.75: 13
        6.75 -     8.44: 6
  Bond angle restraints: 9033
  Sorted by residual:
  angle pdb=" CA  PRO B  17 "
        pdb=" N   PRO B  17 "
        pdb=" CD  PRO B  17 "
      ideal   model   delta    sigma   weight residual
     112.00  107.68    4.32 1.40e+00 5.10e-01 9.51e+00
  angle pdb=" C14 Z5G A 602 "
        pdb=" C13 Z5G A 602 "
        pdb=" S12 Z5G A 602 "
      ideal   model   delta    sigma   weight residual
     121.23  129.67   -8.44 3.00e+00 1.11e-01 7.91e+00
  angle pdb=" C14 Z5G A 601 "
        pdb=" C13 Z5G A 601 "
        pdb=" S12 Z5G A 601 "
      ideal   model   delta    sigma   weight residual
     121.23  129.50   -8.27 3.00e+00 1.11e-01 7.59e+00
  angle pdb=" C   MET A 166 "
        pdb=" N   VAL A 167 "
        pdb=" CA  VAL A 167 "
      ideal   model   delta    sigma   weight residual
     121.97  126.64   -4.67 1.80e+00 3.09e-01 6.74e+00
  angle pdb=" N   ILE A 429 "
        pdb=" CA  ILE A 429 "
        pdb=" C   ILE A 429 "
      ideal   model   delta    sigma   weight residual
     111.91  109.62    2.29 8.90e-01 1.26e+00 6.63e+00
  ... (remaining 9028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.90: 3618
       15.90 -    31.81: 204
       31.81 -    47.71: 52
       47.71 -    63.61: 7
       63.61 -    79.51: 7
  Dihedral angle restraints: 3888
    sinusoidal: 947
      harmonic: 2941
  Sorted by residual:
  dihedral pdb=" CA  PRO B  17 "
           pdb=" C   PRO B  17 "
           pdb=" N   TYR B  18 "
           pdb=" CA  TYR B  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.01  -19.99     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  GLN A 268 "
           pdb=" C   GLN A 268 "
           pdb=" N   ILE A 269 "
           pdb=" CA  ILE A 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.78   17.22     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  VAL A 167 "
           pdb=" C   VAL A 167 "
           pdb=" N   PHE A 168 "
           pdb=" CA  PHE A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.50  -16.50     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 3885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 634
       0.027 -    0.053: 304
       0.053 -    0.080: 114
       0.080 -    0.106: 50
       0.106 -    0.133: 30
  Chirality restraints: 1132
  Sorted by residual:
  chirality pdb=" CB  VAL A 167 "
            pdb=" CA  VAL A 167 "
            pdb=" CG1 VAL A 167 "
            pdb=" CG2 VAL A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CB  VAL A 239 "
            pdb=" CA  VAL A 239 "
            pdb=" CG1 VAL A 239 "
            pdb=" CG2 VAL A 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.40e-01
  chirality pdb=" CA  PRO A 106 "
            pdb=" N   PRO A 106 "
            pdb=" C   PRO A 106 "
            pdb=" CB  PRO A 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 1129 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  16 "    0.076 5.00e-02 4.00e+02   1.13e-01 2.05e+01
        pdb=" N   PRO B  17 "   -0.196 5.00e-02 4.00e+02
        pdb=" CA  PRO B  17 "    0.059 5.00e-02 4.00e+02
        pdb=" CD  PRO B  17 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 290 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.56e+00
        pdb=" N   PRO B 291 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 291 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 291 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 121 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   LYS B 121 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LYS B 121 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 122 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1238
        2.77 -     3.30: 6738
        3.30 -     3.83: 10450
        3.83 -     4.37: 10126
        4.37 -     4.90: 18212
  Nonbonded interactions: 46764
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  18 "
            pdb=" OG  SER B  89 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" ND2 ASN B 125 "
            pdb=" OG  SER B 311 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   ALA A 132 "
            pdb=" OG  SER A 136 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   ALA B 308 "
            pdb=" OG  SER B 311 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" NE2 GLN A  96 "
            pdb=" O   GLY A 432 "
     model   vdw
     2.345 3.120
  ... (remaining 46759 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             0.080
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.450
  Find NCS groups from input model:        0.060
  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:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
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      :  0.004   0.111   6596  Z= 0.270
  Angle     :  0.643   8.435   9033  Z= 0.326
  Chirality :  0.041   0.133   1132
  Planarity :  0.005   0.113   1185
  Dihedral  : 12.062  79.515   1986
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.24 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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:  1.22 (0.27), residues: 1013
  helix:  1.90 (0.21), residues: 624
  sheet:  1.11 (0.98), residues: 34
  loop : -1.27 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 262 
 HIS   0.002   0.000   HIS A 199 
 PHE   0.011   0.001   PHE A  71 
 TYR   0.017   0.001   TYR B 110 
 ARG   0.015   0.001   ARG A 160 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8635 (t0) cc_final: 0.8320 (t0)
REVERT: A   61 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80)
REVERT: A  127 GLU cc_start: 0.7651 (tp30) cc_final: 0.7431 (tp30)
REVERT: B   90 LEU cc_start: 0.7958 (tp) cc_final: 0.7676 (tp)
REVERT: B  140 ILE cc_start: 0.9026 (tp) cc_final: 0.8824 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.1643
  time to fit residues: 41.0195
Evaluate side-chains
  167 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:   40.0000
   chunk 30 optimal weight:    8.9990
   chunk 48 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.210284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.172566 restraints weight = 9413.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.178248 restraints weight = 9357.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.178738 restraints weight = 4572.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6596  Z= 0.273
  Angle     :  0.638   9.152   9033  Z= 0.336
  Chirality :  0.044   0.164   1132
  Planarity :  0.004   0.073   1185
  Dihedral  :  4.810  36.105   1093
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.13 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.76 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1013
  helix:  1.54 (0.20), residues: 651
  sheet:  0.78 (0.95), residues: 34
  loop : -1.50 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  19 
 HIS   0.004   0.001   HIS A 199 
 PHE   0.013   0.002   PHE A 214 
 TYR   0.019   0.002   TYR B  18 
 ARG   0.007   0.001   ARG A 160 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8949 (t0) cc_final: 0.8579 (t0)
REVERT: A  101 LYS cc_start: 0.8698 (tttm) cc_final: 0.8215 (tttm)
REVERT: A  127 GLU cc_start: 0.7827 (tp30) cc_final: 0.7510 (tp30)
REVERT: A  194 MET cc_start: 0.7416 (tpt) cc_final: 0.7214 (tpt)
REVERT: B   47 ILE cc_start: 0.7474 (mm) cc_final: 0.7247 (mm)
REVERT: B   72 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7781 (ptp-170)
REVERT: B   90 LEU cc_start: 0.8394 (tp) cc_final: 0.8158 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 193
  average time/residue: 0.1624
  time to fit residues: 42.2027
Evaluate side-chains
  187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 179
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  279 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 51 optimal weight:   50.0000
   chunk 50 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:   30.0000
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0040
   chunk 17 optimal weight:    6.9990
   chunk 96 optimal weight:    0.0980
   chunk 94 optimal weight:   50.0000
   chunk 86 optimal weight:   30.0000
   chunk 49 optimal weight:   40.0000
   overall best weight:    1.7796

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.212205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.178267 restraints weight = 9515.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.178409 restraints weight = 5831.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.179715 restraints weight = 4542.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6596  Z= 0.177
  Angle     :  0.564   8.769   9033  Z= 0.294
  Chirality :  0.042   0.166   1132
  Planarity :  0.004   0.057   1185
  Dihedral  :  4.565  38.224   1093
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.64 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 26.01 %
    Favored  : 71.12 %
  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:  1.00 (0.27), residues: 1013
  helix:  1.64 (0.21), residues: 657
  sheet:  0.77 (0.91), residues: 34
  loop : -1.46 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  19 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.012   0.001   PHE A 214 
 TYR   0.015   0.001   TYR B  18 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 185
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8855 (t0) cc_final: 0.8468 (t0)
REVERT: A  101 LYS cc_start: 0.8765 (tttm) cc_final: 0.8245 (tttm)
REVERT: A  127 GLU cc_start: 0.7703 (tp30) cc_final: 0.7324 (tp30)
REVERT: A  194 MET cc_start: 0.7269 (tpt) cc_final: 0.6817 (tpt)
REVERT: A  314 GLU cc_start: 0.8695 (pp20) cc_final: 0.8417 (pp20)
REVERT: B   72 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7904 (ptm160)
REVERT: B   90 LEU cc_start: 0.8244 (tp) cc_final: 0.8016 (tp)
REVERT: B  113 ASN cc_start: 0.8171 (m-40) cc_final: 0.7941 (m-40)
REVERT: B  121 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7404 (ttmm)
  outliers start: 12
  outliers final: 9
  residues processed: 189
  average time/residue: 0.1686
  time to fit residues: 42.3217
Evaluate side-chains
  187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 178
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  306 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:   30.0000
   chunk 82 optimal weight:    8.9990
   chunk 47 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.206591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.171754 restraints weight = 9541.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.172372 restraints weight = 5644.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.173382 restraints weight = 4499.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6596  Z= 0.201
  Angle     :  0.576   7.876   9033  Z= 0.301
  Chirality :  0.043   0.171   1132
  Planarity :  0.004   0.058   1185
  Dihedral  :  4.572  38.347   1093
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.84 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 25.54 %
    Favored  : 68.74 %
  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:  1.02 (0.27), residues: 1013
  helix:  1.68 (0.20), residues: 651
  sheet:  0.65 (0.90), residues: 34
  loop : -1.43 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  19 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.011   0.001   PHE A 214 
 TYR   0.017   0.002   TYR A 281 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8891 (t0) cc_final: 0.8542 (t0)
REVERT: A   52 ASN cc_start: 0.7577 (m-40) cc_final: 0.7317 (m110)
REVERT: A  101 LYS cc_start: 0.8800 (tttm) cc_final: 0.8197 (tttm)
REVERT: A  127 GLU cc_start: 0.7754 (tp30) cc_final: 0.7332 (tp30)
REVERT: B   72 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7898 (ptm160)
REVERT: B   90 LEU cc_start: 0.8305 (tp) cc_final: 0.8073 (tp)
REVERT: B  113 ASN cc_start: 0.8182 (m-40) cc_final: 0.7886 (m110)
REVERT: B  121 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7452 (ttmm)
REVERT: B  311 SER cc_start: 0.7657 (OUTLIER) cc_final: 0.7378 (p)
  outliers start: 24
  outliers final: 16
  residues processed: 192
  average time/residue: 0.1655
  time to fit residues: 42.6217
Evaluate side-chains
  192 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:   40.0000
   chunk 60 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.215411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.181138 restraints weight = 9461.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.182242 restraints weight = 5646.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.183247 restraints weight = 4363.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6596  Z= 0.148
  Angle     :  0.544   6.661   9033  Z= 0.283
  Chirality :  0.042   0.168   1132
  Planarity :  0.003   0.058   1185
  Dihedral  :  4.401  36.415   1093
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.05 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 27.92 %
    Favored  : 68.26 %
  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:  1.23 (0.27), residues: 1013
  helix:  1.77 (0.21), residues: 659
  sheet:  0.75 (0.90), residues: 34
  loop : -1.24 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 262 
 HIS   0.002   0.001   HIS A 199 
 PHE   0.010   0.001   PHE A 214 
 TYR   0.015   0.001   TYR B  18 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8722 (t0) cc_final: 0.8372 (t0)
REVERT: A  101 LYS cc_start: 0.8739 (tttm) cc_final: 0.8137 (tttm)
REVERT: A  127 GLU cc_start: 0.7573 (tp30) cc_final: 0.7340 (tp30)
REVERT: A  191 GLN cc_start: 0.7673 (tp40) cc_final: 0.7455 (tp-100)
REVERT: A  238 MET cc_start: 0.8203 (tmm) cc_final: 0.7332 (ttt)
REVERT: B   41 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8095 (mmtt)
REVERT: B   72 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7894 (ptm160)
REVERT: B   90 LEU cc_start: 0.8089 (tp) cc_final: 0.7851 (tp)
REVERT: B  127 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7265 (tt0)
  outliers start: 16
  outliers final: 8
  residues processed: 190
  average time/residue: 0.1656
  time to fit residues: 42.2383
Evaluate side-chains
  184 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 175
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 80 optimal weight:   30.0000
   chunk 83 optimal weight:   30.0000
   chunk 37 optimal weight:    0.9980
   chunk 71 optimal weight:   10.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
B 113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.209482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.175274 restraints weight = 9446.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.176848 restraints weight = 5542.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.177553 restraints weight = 4177.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6596  Z= 0.193
  Angle     :  0.580  10.526   9033  Z= 0.300
  Chirality :  0.043   0.177   1132
  Planarity :  0.003   0.057   1185
  Dihedral  :  4.513  37.000   1093
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.74 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 30.55 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.27), residues: 1013
  helix:  1.73 (0.21), residues: 655
  sheet:  0.73 (0.89), residues: 34
  loop : -1.36 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 262 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.011   0.001   PHE A 214 
 TYR   0.014   0.002   TYR A 281 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8883 (t0) cc_final: 0.8561 (t0)
REVERT: A  101 LYS cc_start: 0.8754 (tttm) cc_final: 0.8144 (tttm)
REVERT: A  103 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5377 (pp)
REVERT: A  127 GLU cc_start: 0.7686 (tp30) cc_final: 0.7466 (tp30)
REVERT: A  191 GLN cc_start: 0.7714 (tp40) cc_final: 0.7505 (tp-100)
REVERT: B   41 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8252 (mmtt)
REVERT: B   72 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7923 (ptm160)
REVERT: B   90 LEU cc_start: 0.8164 (tp) cc_final: 0.7932 (tp)
REVERT: B  287 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8246 (mt)
REVERT: B  311 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7606 (p)
  outliers start: 19
  outliers final: 11
  residues processed: 189
  average time/residue: 0.1672
  time to fit residues: 42.6786
Evaluate side-chains
  189 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  243 ASN
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  289 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 94 optimal weight:   50.0000
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 92 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 78 optimal weight:   50.0000
   chunk 9 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.202413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.163338 restraints weight = 9597.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.170319 restraints weight = 8501.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.169817 restraints weight = 4052.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   6596  Z= 0.285
  Angle     :  0.636   8.462   9033  Z= 0.340
  Chirality :  0.045   0.182   1132
  Planarity :  0.004   0.058   1185
  Dihedral  :  4.917  37.201   1093
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.43 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 30.79 %
    Favored  : 63.96 %
  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:  0.74 (0.27), residues: 1013
  helix:  1.44 (0.20), residues: 653
  sheet:  0.66 (0.88), residues: 34
  loop : -1.53 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 262 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.013   0.001   PHE A 214 
 TYR   0.018   0.002   TYR A 281 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.9034 (t0) cc_final: 0.8703 (t0)
REVERT: A  101 LYS cc_start: 0.8804 (tttm) cc_final: 0.8230 (tttm)
REVERT: A  103 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5933 (pp)
REVERT: A  127 GLU cc_start: 0.7883 (tp30) cc_final: 0.7455 (tp30)
REVERT: A  304 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8074 (tpp-160)
REVERT: B   72 ARG cc_start: 0.8342 (ttm170) cc_final: 0.8031 (ptm160)
REVERT: B   90 LEU cc_start: 0.8430 (tp) cc_final: 0.8224 (tp)
REVERT: B  121 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7501 (ttmm)
REVERT: B  140 ILE cc_start: 0.9151 (tp) cc_final: 0.8906 (tp)
REVERT: B  287 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8572 (mm)
  outliers start: 22
  outliers final: 17
  residues processed: 194
  average time/residue: 0.1567
  time to fit residues: 40.9014
Evaluate side-chains
  188 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   94 ILE
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  204 SER
Chi-restraints excluded: chain A residue  208 ASN
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  311 SER
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 87 optimal weight:    6.9990
   chunk 67 optimal weight:    0.8980
   chunk 99 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.208935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.174523 restraints weight = 9563.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.174873 restraints weight = 5593.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.175819 restraints weight = 4558.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6596  Z= 0.177
  Angle     :  0.587  10.970   9033  Z= 0.303
  Chirality :  0.043   0.194   1132
  Planarity :  0.003   0.057   1185
  Dihedral  :  4.635  34.916   1093
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.84 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 33.89 %
    Favored  : 63.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.98 (0.27), residues: 1013
  helix:  1.63 (0.21), residues: 655
  sheet:  0.68 (0.88), residues: 34
  loop : -1.42 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 262 
 HIS   0.002   0.001   HIS A 199 
 PHE   0.009   0.001   PHE A 214 
 TYR   0.013   0.001   TYR B  18 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 175
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8878 (t0) cc_final: 0.8531 (t0)
REVERT: A   97 GLU cc_start: 0.7910 (tt0) cc_final: 0.7695 (tt0)
REVERT: A  101 LYS cc_start: 0.8769 (tttm) cc_final: 0.8159 (tttm)
REVERT: A  127 GLU cc_start: 0.7673 (tp30) cc_final: 0.7281 (tp30)
REVERT: A  304 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.7957 (tpp-160)
REVERT: B   41 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8158 (mmtt)
REVERT: B   72 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7835 (ptm160)
REVERT: B   90 LEU cc_start: 0.8172 (tp) cc_final: 0.7954 (tp)
  outliers start: 12
  outliers final: 11
  residues processed: 184
  average time/residue: 0.1646
  time to fit residues: 40.8623
Evaluate side-chains
  185 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 174
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 78 optimal weight:   40.0000
   chunk 71 optimal weight:    0.0170
   chunk 29 optimal weight:    7.9990
   chunk 67 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 49 optimal weight:   50.0000
   chunk 64 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.4822

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.212386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.178374 restraints weight = 9588.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.179778 restraints weight = 5629.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.180616 restraints weight = 4185.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6596  Z= 0.180
  Angle     :  0.596  10.523   9033  Z= 0.304
  Chirality :  0.043   0.200   1132
  Planarity :  0.003   0.058   1185
  Dihedral  :  4.597  35.457   1093
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.74 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 33.65 %
    Favored  : 63.01 %
  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:  1.03 (0.27), residues: 1013
  helix:  1.66 (0.21), residues: 655
  sheet:  0.76 (0.88), residues: 34
  loop : -1.40 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 262 
 HIS   0.002   0.001   HIS A 199 
 PHE   0.010   0.001   PHE A 214 
 TYR   0.014   0.001   TYR A 281 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.8865 (t0) cc_final: 0.8535 (t0)
REVERT: A  101 LYS cc_start: 0.8744 (tttm) cc_final: 0.8154 (tttm)
REVERT: A  103 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5269 (pp)
REVERT: A  127 GLU cc_start: 0.7558 (tp30) cc_final: 0.7268 (tp30)
REVERT: A  304 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7936 (tpp-160)
REVERT: A  306 LEU cc_start: 0.6999 (mt) cc_final: 0.6218 (tt)
REVERT: B   41 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8158 (mmtt)
REVERT: B   72 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7887 (ptm160)
REVERT: B   90 LEU cc_start: 0.8106 (tp) cc_final: 0.7885 (tp)
  outliers start: 14
  outliers final: 11
  residues processed: 185
  average time/residue: 0.1664
  time to fit residues: 41.5956
Evaluate side-chains
  186 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  243 ASN
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    9.9990
   chunk 85 optimal weight:   10.0000
   chunk 74 optimal weight:    4.9990
   chunk 53 optimal weight:   40.0000
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    0.0980
   chunk 83 optimal weight:    8.9990
   overall best weight:    4.0188

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

Flipped N/Q/H residues before XYZ refinement:
A 208 ASN
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.209815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.174375 restraints weight = 9705.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.174779 restraints weight = 5833.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.176070 restraints weight = 4274.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074   6596  Z= 0.313
  Angle     :  0.679  10.132   9033  Z= 0.361
  Chirality :  0.046   0.192   1132
  Planarity :  0.004   0.057   1185
  Dihedral  :  4.987  36.665   1093
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.23 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 34.13 %
    Favored  : 62.77 %
  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:  0.64 (0.26), residues: 1013
  helix:  1.40 (0.20), residues: 650
  sheet:  0.67 (0.87), residues: 34
  loop : -1.61 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 159 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.014   0.002   PHE A 214 
 TYR   0.024   0.002   TYR B  99 
 ARG   0.003   0.000   ARG B 304 

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

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

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2026 Ramachandran restraints generated.
    1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
REVERT: A   32 ASN cc_start: 0.9078 (t0) cc_final: 0.8724 (t0)
REVERT: A  101 LYS cc_start: 0.8786 (tttm) cc_final: 0.8231 (tttm)
REVERT: A  103 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5614 (pp)
REVERT: A  127 GLU cc_start: 0.7858 (tp30) cc_final: 0.7428 (tp30)
REVERT: A  304 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.8060 (tpp-160)
REVERT: B   72 ARG cc_start: 0.8389 (ttm170) cc_final: 0.7986 (ptm160)
REVERT: B  121 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7657 (ttmm)
REVERT: B  140 ILE cc_start: 0.9152 (tp) cc_final: 0.8903 (tp)
  outliers start: 13
  outliers final: 11
  residues processed: 178
  average time/residue: 0.1689
  time to fit residues: 40.3723
Evaluate side-chains
  179 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  312 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  312 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 52 optimal weight:   20.0000
   chunk 84 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    1.4146

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.216433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.173606 restraints weight = 9694.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.177962 restraints weight = 5704.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.181043 restraints weight = 3843.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6977
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6596  Z= 0.186
  Angle     :  0.634  10.971   9033  Z= 0.322
  Chirality :  0.044   0.200   1132
  Planarity :  0.003   0.057   1185
  Dihedral  :  4.712  34.863   1093
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  4.74 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 34.37 %
    Favored  : 62.53 %
  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:  0.89 (0.27), residues: 1013
  helix:  1.53 (0.21), residues: 655
  sheet:  0.69 (0.88), residues: 34
  loop : -1.41 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 262 
 HIS   0.002   0.001   HIS A 199 
 PHE   0.010   0.001   PHE A 214 
 TYR   0.013   0.001   TYR A  82 
 ARG   0.004   0.000   ARG B 304 

===============================================================================
Job complete
usr+sys time: 1934.42 seconds
wall clock time: 34 minutes 9.45 seconds (2049.45 seconds total)