Starting phenix.real_space_refine
on Thu Mar 13 17:50:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pqx_13606/03_2025/7pqx_13606.cif"
  }
  resolution = 3.08
  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=   0.001 sd=   0.105
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      24      5.16       5
     C    5784      2.51       5
     N    1572      2.21       5
     O    1652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9032
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4516
          Classifications: {'peptide': 580}
          Link IDs: {'PTRANS': 17, 'TRANS': 562}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.53, per 1000 atoms: 0.94
  Number of scatterers: 9032
  At special positions: 0
  Unit cell: (80.704, 118.976, 141.44, 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      24     16.00
     O    1652      8.00
     N    1572      7.00
     C    5784      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: 2.38
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2164

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      67.3% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 103
      removed outlier: 4.442A  pdb=" N   GLN A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 144
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 147 through 152
      removed outlier: 3.520A  pdb=" N   GLY A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 205
      removed outlier: 3.757A  pdb=" N   GLN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
      removed outlier: 3.729A  pdb=" N   HIS A 211 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 239
    Processing helix  chain 'A' and resid 240 through 259
    Processing helix  chain 'A' and resid 260 through 309
      removed outlier: 4.074A  pdb=" N   ALA A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 286 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LYS A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   PHE A 288 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ASN A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 316
      removed outlier: 3.614A  pdb=" N   PHE A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 371
      removed outlier: 3.711A  pdb=" N   GLU A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER A 336 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 339 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 392
      removed outlier: 3.605A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL A 381 " --> pdb=" O   VAL A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 398
      removed outlier: 4.021A  pdb=" N   GLY A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 395 through 398'
    Processing helix  chain 'A' and resid 399 through 418
      removed outlier: 3.754A  pdb=" N   ARG A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 488
    Processing helix  chain 'A' and resid 509 through 516
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 543 through 554
    Processing helix  chain 'A' and resid 556 through 562
    Processing helix  chain 'A' and resid 565 through 568
      removed outlier: 3.612A  pdb=" N   GLN A 568 " --> pdb=" O   HIS A 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 565 through 568'
    Processing helix  chain 'A' and resid 579 through 595
    Processing helix  chain 'A' and resid 609 through 625
    Processing helix  chain 'A' and resid 660 through 666
      removed outlier: 3.957A  pdb=" N   GLU A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 674
      removed outlier: 4.309A  pdb=" N   GLU A 673 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 103
    Processing helix  chain 'B' and resid 109 through 144
      Proline residue:  B 134  - end of helix
    Processing helix  chain 'B' and resid 147 through 152
      removed outlier: 3.521A  pdb=" N   GLY B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 205
      removed outlier: 3.757A  pdb=" N   GLN B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 213
      removed outlier: 3.730A  pdb=" N   HIS B 211 " --> pdb=" O   ASP B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 239
    Processing helix  chain 'B' and resid 240 through 259
    Processing helix  chain 'B' and resid 260 through 309
      removed outlier: 4.074A  pdb=" N   ALA B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR B 286 " --> pdb=" O   THR B 282 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   LYS B 287 " --> pdb=" O   ALA B 283 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   PHE B 288 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN B 309 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 316
      removed outlier: 3.614A  pdb=" N   PHE B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 371
      removed outlier: 3.710A  pdb=" N   GLU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 392
      removed outlier: 3.605A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL B 381 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 398
      removed outlier: 4.021A  pdb=" N   GLY B 398 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 395 through 398'
    Processing helix  chain 'B' and resid 399 through 418
      removed outlier: 3.754A  pdb=" N   ARG B 405 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 488
    Processing helix  chain 'B' and resid 509 through 516
    Processing helix  chain 'B' and resid 531 through 537
    Processing helix  chain 'B' and resid 543 through 554
    Processing helix  chain 'B' and resid 556 through 562
    Processing helix  chain 'B' and resid 565 through 568
      removed outlier: 3.611A  pdb=" N   GLN B 568 " --> pdb=" O   HIS B 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 565 through 568'
    Processing helix  chain 'B' and resid 579 through 595
    Processing helix  chain 'B' and resid 609 through 625
    Processing helix  chain 'B' and resid 660 through 666
      removed outlier: 3.958A  pdb=" N   GLU B 666 " --> pdb=" O   ARG B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 674
      removed outlier: 4.309A  pdb=" N   GLU B 673 " --> pdb=" O   VAL B 670 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG A 458 " --> pdb=" O   PHE A 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE A 448 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL A 446 " --> pdb=" O   GLN A 495 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLN A 495 " --> pdb=" O   VAL A 446 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 517 through 518
      removed outlier: 6.398A  pdb=" N   GLY A 518 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ASP A 602 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU A 599 " --> pdb=" O   LEU A 632 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   VAL A 634 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 634 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A 635 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ALA A 471 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU A 650 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   VAL A 473 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE A 647 " --> pdb=" O   GLN A 658 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   GLN A 658 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL A 649 " --> pdb=" O   VAL A 656 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   VAL A 656 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A 654 " --> pdb=" O   LYS A 651 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 530
    Processing sheet with id=AA5, first strand: chain 'B' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 460
      removed outlier: 5.481A  pdb=" N   ARG B 458 " --> pdb=" O   PHE B 448 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   PHE B 448 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   VAL B 446 " --> pdb=" O   GLN B 495 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   GLN B 495 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 517 through 518
      removed outlier: 6.398A  pdb=" N   GLY B 518 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ASP B 602 " --> pdb=" O   GLY B 518 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LEU B 599 " --> pdb=" O   LEU B 632 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   VAL B 634 " --> pdb=" O   LEU B 599 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE B 601 " --> pdb=" O   VAL B 634 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA B 635 " --> pdb=" O   VAL B 472 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   ALA B 471 " --> pdb=" O   ILE B 648 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LEU B 650 " --> pdb=" O   ALA B 471 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   VAL B 473 " --> pdb=" O   LEU B 650 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE B 647 " --> pdb=" O   GLN B 658 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   GLN B 658 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   VAL B 649 " --> pdb=" O   VAL B 656 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   VAL B 656 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B 654 " --> pdb=" O   LYS B 651 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 529 through 530

    590 hydrogen bonds defined for protein.
    1746 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: 2.85

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2683
        1.34 -     1.45: 1415
        1.45 -     1.57: 5054
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" C   TRP A 563 "
       pdb=" N   PRO A 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.30e-02 5.92e+03 6.42e+00
  bond pdb=" C   TRP B 563 "
       pdb=" N   PRO B 564 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 1.30e-02 5.92e+03 6.00e+00
  bond pdb=" CB  ARG B 170 "
       pdb=" CG  ARG B 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.454  0.066 3.00e-02 1.11e+03 4.81e+00
  bond pdb=" CB  ARG A 170 "
       pdb=" CG  ARG A 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.455  0.065 3.00e-02 1.11e+03 4.72e+00
  bond pdb=" CB  THR B 281 "
       pdb=" CG2 THR B 281 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.58e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 11862
        2.28 -     4.55: 498
        4.55 -     6.83: 66
        6.83 -     9.10: 40
        9.10 -    11.38: 4
  Bond angle restraints: 12470
  Sorted by residual:
  angle pdb=" N   GLU A 622 "
        pdb=" CA  GLU A 622 "
        pdb=" CB  GLU A 622 "
      ideal   model   delta    sigma   weight residual
     110.39  118.50   -8.11 1.66e+00 3.63e-01 2.39e+01
  angle pdb=" N   GLU B 622 "
        pdb=" CA  GLU B 622 "
        pdb=" CB  GLU B 622 "
      ideal   model   delta    sigma   weight residual
     110.39  118.46   -8.07 1.66e+00 3.63e-01 2.36e+01
  angle pdb=" C   GLU A 444 "
        pdb=" N   ASN A 445 "
        pdb=" CA  ASN A 445 "
      ideal   model   delta    sigma   weight residual
     121.54  129.16   -7.62 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" OG1 THR B 482 "
        pdb=" CB  THR B 482 "
        pdb=" CG2 THR B 482 "
      ideal   model   delta    sigma   weight residual
     109.30  101.32    7.98 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" C   GLU B 444 "
        pdb=" N   ASN B 445 "
        pdb=" CA  ASN B 445 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  ... (remaining 12465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 4884
       16.44 -    32.87: 498
       32.87 -    49.31: 110
       49.31 -    65.74: 14
       65.74 -    82.18: 10
  Dihedral angle restraints: 5516
    sinusoidal: 2156
      harmonic: 3360
  Sorted by residual:
  dihedral pdb=" CA  ASP B 502 "
           pdb=" C   ASP B 502 "
           pdb=" N   GLN B 503 "
           pdb=" CA  GLN B 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.22   22.78     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASP A 502 "
           pdb=" C   ASP A 502 "
           pdb=" N   GLN A 503 "
           pdb=" CA  GLN A 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.23   22.77     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  TYR B 451 "
           pdb=" C   TYR B 451 "
           pdb=" N   PRO B 452 "
           pdb=" CA  PRO B 452 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.99  -22.01     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 5513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 874
       0.048 -    0.095: 402
       0.095 -    0.143: 137
       0.143 -    0.190: 35
       0.190 -    0.238: 16
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CG  LEU B 487 "
            pdb=" CB  LEU B 487 "
            pdb=" CD1 LEU B 487 "
            pdb=" CD2 LEU B 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.83    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  ILE B 641 "
            pdb=" CA  ILE B 641 "
            pdb=" CG1 ILE B 641 "
            pdb=" CG2 ILE B 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CG  LEU A 487 "
            pdb=" CB  LEU A 487 "
            pdb=" CD1 LEU A 487 "
            pdb=" CD2 LEU A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 388 "    0.030 2.00e-02 2.50e+03   2.21e-02 8.55e+00
        pdb=" CG  PHE A 388 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 388 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 388 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 388 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 388 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 388 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 388 "   -0.030 2.00e-02 2.50e+03   2.21e-02 8.52e+00
        pdb=" CG  PHE B 388 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 388 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 388 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 388 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 388 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 388 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 454 "    0.045 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A 455 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 455 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 455 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2706
        2.82 -     3.34: 8629
        3.34 -     3.86: 15223
        3.86 -     4.38: 17097
        4.38 -     4.90: 29971
  Nonbonded interactions: 73626
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 206 "
            pdb=" OH  TYR B 310 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   GLU B 558 "
            pdb=" OG  SER B 562 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   GLU A 558 "
            pdb=" OG  SER A 562 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   GLY A 566 "
            pdb=" OG1 THR A 569 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   GLY B 566 "
            pdb=" OG1 THR B 569 "
     model   vdw
     2.312 3.040
  ... (remaining 73621 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 individual isotropic
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:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.890
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
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      :  0.010   0.103   9196  Z= 0.600
  Angle     :  1.108  11.381  12470  Z= 0.605
  Chirality :  0.063   0.238   1464
  Planarity :  0.007   0.069   1584
  Dihedral  : 14.204  82.177   3352
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.13 (0.21), residues: 1156
  helix: -1.08 (0.16), residues: 740
  sheet:  0.20 (0.67), residues: 60
  loop : -2.15 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 284 
 HIS   0.007   0.002   HIS B 132 
 PHE   0.038   0.005   PHE A 388 
 TYR   0.028   0.003   TYR A 274 
 ARG   0.016   0.001   ARG B 425 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.899 
Fit side-chains
REVERT: A  532 GLU cc_start: 0.7287 (tp30) cc_final: 0.6662 (tp30)
REVERT: B  401 TYR cc_start: 0.6469 (t80) cc_final: 0.6267 (t80)
REVERT: B  532 GLU cc_start: 0.7289 (tp30) cc_final: 0.6705 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2048
  time to fit residues: 34.3044
Evaluate side-chains
  96 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0370
   chunk 90 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 67 optimal weight:    0.5980
   chunk 105 optimal weight:    9.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** 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 = 0.4203 r_free = 0.4203 target = 0.190666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.117592 restraints weight = 10201.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 2.13
r_work: 0.3239 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9196  Z= 0.196
  Angle     :  0.600   7.793  12470  Z= 0.319
  Chirality :  0.043   0.155   1464
  Planarity :  0.004   0.050   1584
  Dihedral  :  5.094  21.202   1266
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1156
  helix:  0.58 (0.18), residues: 748
  sheet:  0.07 (0.66), residues: 60
  loop : -1.70 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 284 
 HIS   0.003   0.001   HIS B 132 
 PHE   0.028   0.002   PHE A 355 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 536 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8743 (p) cc_final: 0.8345 (m)
REVERT: A  522 GLN cc_start: 0.8562 (tt0) cc_final: 0.8195 (tp40)
REVERT: A  617 MET cc_start: 0.9214 (tpp) cc_final: 0.8872 (tpp)
REVERT: B  522 GLN cc_start: 0.8583 (tt0) cc_final: 0.8209 (tp40)
REVERT: B  617 MET cc_start: 0.9191 (tpp) cc_final: 0.8842 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1875
  time to fit residues: 35.3595
Evaluate side-chains
  107 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 555 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.189778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.116491 restraints weight = 10259.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.16
r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9196  Z= 0.200
  Angle     :  0.579   8.040  12470  Z= 0.302
  Chirality :  0.043   0.158   1464
  Planarity :  0.003   0.041   1584
  Dihedral  :  4.747  19.645   1266
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.40 %
    Favored  : 88.67 %
  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:  0.59 (0.25), residues: 1156
  helix:  1.26 (0.19), residues: 748
  sheet:  0.24 (0.67), residues: 60
  loop : -1.47 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 284 
 HIS   0.005   0.001   HIS A 555 
 PHE   0.023   0.002   PHE B 355 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.002   0.000   ARG B 425 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A  349 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8378 (m)
REVERT: A  522 GLN cc_start: 0.8560 (tt0) cc_final: 0.8127 (tp40)
REVERT: A  617 MET cc_start: 0.9208 (tpp) cc_final: 0.8873 (tpp)
REVERT: B  522 GLN cc_start: 0.8569 (tt0) cc_final: 0.8131 (tp40)
REVERT: B  617 MET cc_start: 0.9201 (tpp) cc_final: 0.8887 (tpp)
  outliers start: 9
  outliers final: 2
  residues processed: 113
  average time/residue: 0.2222
  time to fit residues: 38.5015
Evaluate side-chains
  105 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.189092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116010 restraints weight = 10127.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.10
r_work: 0.3215 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9196  Z= 0.228
  Angle     :  0.559   6.968  12470  Z= 0.294
  Chirality :  0.043   0.151   1464
  Planarity :  0.003   0.035   1584
  Dihedral  :  4.637  18.745   1266
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.68 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.78 (0.25), residues: 1156
  helix:  1.37 (0.19), residues: 760
  sheet:  0.39 (0.69), residues: 60
  loop : -1.44 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 284 
 HIS   0.005   0.001   HIS A 555 
 PHE   0.025   0.002   PHE B 448 
 TYR   0.013   0.001   TYR B 274 
 ARG   0.002   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.280 
Fit side-chains
REVERT: A  349 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8472 (m)
REVERT: A  355 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7240 (t80)
REVERT: A  401 TYR cc_start: 0.7131 (t80) cc_final: 0.6889 (t80)
REVERT: A  511 GLU cc_start: 0.7481 (pm20) cc_final: 0.7219 (mm-30)
REVERT: A  522 GLN cc_start: 0.8478 (tt0) cc_final: 0.8065 (tp40)
REVERT: A  617 MET cc_start: 0.9217 (tpp) cc_final: 0.8908 (tpp)
REVERT: B  355 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7218 (t80)
REVERT: B  511 GLU cc_start: 0.7478 (pm20) cc_final: 0.7205 (mm-30)
REVERT: B  522 GLN cc_start: 0.8483 (tt0) cc_final: 0.8072 (tp40)
REVERT: B  617 MET cc_start: 0.9218 (tpp) cc_final: 0.8906 (tpp)
  outliers start: 11
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1682
  time to fit residues: 28.7098
Evaluate side-chains
  117 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 115 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0870
   chunk 101 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0770
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
A 557 HIS
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.191553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.118858 restraints weight = 10213.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.12
r_work: 0.3251 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9196  Z= 0.160
  Angle     :  0.521   6.828  12470  Z= 0.274
  Chirality :  0.041   0.146   1464
  Planarity :  0.003   0.031   1584
  Dihedral  :  4.424  18.151   1266
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.99 %
    Favored  : 85.14 %
  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:  1.14 (0.25), residues: 1156
  helix:  1.71 (0.19), residues: 748
  sheet:  0.41 (0.69), residues: 60
  loop : -1.30 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 284 
 HIS   0.006   0.001   HIS B 555 
 PHE   0.017   0.001   PHE B 355 
 TYR   0.008   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 590 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (m)
REVERT: A  355 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7186 (t80)
REVERT: A  522 GLN cc_start: 0.8528 (tt0) cc_final: 0.7719 (tp40)
REVERT: A  603 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7838 (pt0)
REVERT: A  617 MET cc_start: 0.9222 (tpp) cc_final: 0.8913 (tpp)
REVERT: B  317 ASN cc_start: 0.8323 (m-40) cc_final: 0.8111 (t0)
REVERT: B  355 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7172 (t80)
REVERT: B  522 GLN cc_start: 0.8522 (tt0) cc_final: 0.7725 (tp40)
REVERT: B  603 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7830 (pt0)
REVERT: B  617 MET cc_start: 0.9213 (tpp) cc_final: 0.8910 (tpp)
  outliers start: 18
  outliers final: 7
  residues processed: 125
  average time/residue: 0.1523
  time to fit residues: 30.3095
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0000
   chunk 86 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS
A 557 HIS
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.191044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.118199 restraints weight = 10090.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.08
r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9196  Z= 0.182
  Angle     :  0.537   7.205  12470  Z= 0.282
  Chirality :  0.042   0.156   1464
  Planarity :  0.003   0.027   1584
  Dihedral  :  4.357  17.264   1266
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.66 %
    Favored  : 83.37 %
  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:  1.29 (0.25), residues: 1156
  helix:  1.82 (0.19), residues: 748
  sheet:  0.48 (0.69), residues: 60
  loop : -1.24 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.029   0.002   PHE A 448 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.002   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8318 (m)
REVERT: A  355 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7199 (t80)
REVERT: A  522 GLN cc_start: 0.8454 (tt0) cc_final: 0.7590 (tp40)
REVERT: A  545 GLU cc_start: 0.8050 (pm20) cc_final: 0.7798 (pm20)
REVERT: A  603 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7725 (pt0)
REVERT: A  617 MET cc_start: 0.9225 (tpp) cc_final: 0.8922 (tpp)
REVERT: B  317 ASN cc_start: 0.8238 (m-40) cc_final: 0.8035 (t0)
REVERT: B  355 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7178 (t80)
REVERT: B  522 GLN cc_start: 0.8473 (tt0) cc_final: 0.7615 (tp40)
REVERT: B  545 GLU cc_start: 0.8045 (pm20) cc_final: 0.7792 (pm20)
REVERT: B  603 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7716 (pt0)
REVERT: B  617 MET cc_start: 0.9221 (tpp) cc_final: 0.8935 (tpp)
  outliers start: 19
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1454
  time to fit residues: 28.0721
Evaluate side-chains
  119 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 41 optimal weight:    0.3980
   chunk 66 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 96 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 HIS
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.191132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.118002 restraints weight = 10211.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.11
r_work: 0.3239 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9196  Z= 0.191
  Angle     :  0.540   7.461  12470  Z= 0.283
  Chirality :  0.041   0.143   1464
  Planarity :  0.003   0.026   1584
  Dihedral  :  4.316  16.604   1266
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.18 %
    Favored  : 83.26 %
  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:  1.35 (0.25), residues: 1156
  helix:  1.88 (0.19), residues: 748
  sheet:  0.55 (0.70), residues: 60
  loop : -1.25 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.017   0.001   PHE B 355 
 TYR   0.012   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 458 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 ASP cc_start: 0.7653 (p0) cc_final: 0.7208 (p0)
REVERT: A  349 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8332 (m)
REVERT: A  355 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7190 (t80)
REVERT: A  522 GLN cc_start: 0.8435 (tt0) cc_final: 0.7552 (tp40)
REVERT: A  603 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7664 (pt0)
REVERT: A  617 MET cc_start: 0.9223 (tpp) cc_final: 0.8928 (tpp)
REVERT: B  317 ASN cc_start: 0.8224 (m-40) cc_final: 0.8012 (t0)
REVERT: B  355 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7182 (t80)
REVERT: B  522 GLN cc_start: 0.8447 (tt0) cc_final: 0.7557 (tp40)
REVERT: B  603 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7672 (pt0)
REVERT: B  617 MET cc_start: 0.9218 (tpp) cc_final: 0.8934 (tpp)
  outliers start: 15
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1812
  time to fit residues: 33.1442
Evaluate side-chains
  116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 57 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 108 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 HIS
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.191338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.118680 restraints weight = 10309.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.10
r_work: 0.3243 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9196  Z= 0.183
  Angle     :  0.542   7.544  12470  Z= 0.282
  Chirality :  0.041   0.140   1464
  Planarity :  0.003   0.025   1584
  Dihedral  :  4.279  17.539   1266
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.97 %
    Favored  : 83.26 %
  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:  1.45 (0.26), residues: 1156
  helix:  1.94 (0.19), residues: 748
  sheet:  0.65 (0.71), residues: 60
  loop : -1.21 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.028   0.002   PHE B 448 
 TYR   0.010   0.001   TYR B 274 
 ARG   0.001   0.000   ARG A 170 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8321 (m)
REVERT: A  355 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7199 (t80)
REVERT: A  522 GLN cc_start: 0.8436 (tt0) cc_final: 0.7941 (tp40)
REVERT: A  617 MET cc_start: 0.9214 (tpp) cc_final: 0.8933 (tpp)
REVERT: B  317 ASN cc_start: 0.8215 (m-40) cc_final: 0.7993 (t0)
REVERT: B  355 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7198 (t80)
REVERT: B  522 GLN cc_start: 0.8431 (tt0) cc_final: 0.7518 (tp40)
REVERT: B  603 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7541 (pt0)
REVERT: B  617 MET cc_start: 0.9215 (tpp) cc_final: 0.8939 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1666
  time to fit residues: 29.1681
Evaluate side-chains
  116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 58 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 HIS
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 503 GLN
B 557 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.190492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120246 restraints weight = 10178.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.50
r_work: 0.3214 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9196  Z= 0.214
  Angle     :  0.562   7.625  12470  Z= 0.293
  Chirality :  0.042   0.151   1464
  Planarity :  0.003   0.028   1584
  Dihedral  :  4.308  17.360   1266
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.66 %
    Favored  : 83.16 %
  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:  1.37 (0.25), residues: 1156
  helix:  1.83 (0.19), residues: 758
  sheet:  0.64 (0.70), residues: 60
  loop : -1.20 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.028   0.002   PHE A 210 
 TYR   0.012   0.001   TYR A 274 
 ARG   0.006   0.000   ARG A 458 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8472 (m)
REVERT: A  355 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7194 (t80)
REVERT: A  522 GLN cc_start: 0.8427 (tt0) cc_final: 0.7924 (tp40)
REVERT: A  617 MET cc_start: 0.9213 (tpp) cc_final: 0.8937 (tpp)
REVERT: B  319 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8090 (mp0)
REVERT: B  355 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7240 (t80)
REVERT: B  522 GLN cc_start: 0.8446 (tt0) cc_final: 0.7941 (tp40)
REVERT: B  617 MET cc_start: 0.9218 (tpp) cc_final: 0.8941 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1536
  time to fit residues: 27.8770
Evaluate side-chains
  116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 109 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 541 ASN
A 557 HIS
** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 ASN
B 557 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.190751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.122128 restraints weight = 10348.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.69
r_work: 0.3180 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9196  Z= 0.211
  Angle     :  0.567   7.740  12470  Z= 0.296
  Chirality :  0.042   0.147   1464
  Planarity :  0.003   0.028   1584
  Dihedral  :  4.353  17.280   1266
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.45 %
    Favored  : 83.37 %
  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:  1.39 (0.25), residues: 1156
  helix:  1.85 (0.19), residues: 758
  sheet:  0.60 (0.70), residues: 60
  loop : -1.18 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.007   0.001   HIS A 555 
 PHE   0.025   0.002   PHE B 448 
 TYR   0.012   0.001   TYR B 274 
 ARG   0.006   0.000   ARG B 458 

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8104 (mp0)
REVERT: A  349 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8425 (m)
REVERT: A  355 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7185 (t80)
REVERT: A  522 GLN cc_start: 0.8422 (tt0) cc_final: 0.7908 (tp40)
REVERT: A  617 MET cc_start: 0.9218 (tpp) cc_final: 0.8945 (tpp)
REVERT: B  319 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8088 (mp0)
REVERT: B  355 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7211 (t80)
REVERT: B  503 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6908 (pm20)
REVERT: B  522 GLN cc_start: 0.8411 (tt0) cc_final: 0.7904 (tp40)
REVERT: B  617 MET cc_start: 0.9218 (tpp) cc_final: 0.8944 (tpp)
  outliers start: 21
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2232
  time to fit residues: 41.3334
Evaluate side-chains
  118 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 GLU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  355 PHE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  422 VAL
Chi-restraints excluded: chain A residue  503 GLN
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  319 GLU
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  391 SER
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  503 GLN
Chi-restraints excluded: chain B residue  513 LEU
Chi-restraints excluded: chain B residue  530 THR
Chi-restraints excluded: chain B residue  531 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    0.3980
   chunk 59 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 503 GLN
A 541 ASN
A 557 HIS
** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 ASN
B 557 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.190986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.122501 restraints weight = 10261.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 2.64
r_work: 0.3201 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9196  Z= 0.205
  Angle     :  0.569   9.537  12470  Z= 0.296
  Chirality :  0.042   0.140   1464
  Planarity :  0.003   0.029   1584
  Dihedral  :  4.289  16.850   1266
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.28 %
    Favored  : 83.06 %
  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:  1.46 (0.25), residues: 1156
  helix:  1.90 (0.19), residues: 758
  sheet:  0.62 (0.69), residues: 60
  loop : -1.15 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 284 
 HIS   0.006   0.001   HIS A 555 
 PHE   0.017   0.001   PHE B 355 
 TYR   0.011   0.001   TYR B 274 
 ARG   0.007   0.000   ARG B 458 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6218.74 seconds
wall clock time: 111 minutes 10.81 seconds (6670.81 seconds total)