Starting phenix.real_space_refine
on Fri May 16 21:44:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pr2_17832/05_2025/8pr2_17832.cif"
  }
  resolution = 3.8
  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=   0.000 sd=   0.001
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      51      5.16       5
     C    9396      2.51       5
     N    2679      2.21       5
     O    2780      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14906
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 917
          Classifications: {'peptide': 106}
          Link IDs: {'TRANS': 105}
    Chain: "C"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 917
          Classifications: {'peptide': 106}
          Link IDs: {'TRANS': 105}
    Chain: "f"
      Number of atoms: 5865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 711, 5865
          Classifications: {'peptide': 711}
          Link IDs: {'PTRANS': 19, 'TRANS': 691}
          Chain breaks: 2
    Chain: "h"
      Number of atoms: 2897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2897
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 17, 'TRANS': 353}
    Chain: "j"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 202
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "m"
      Number of atoms: 4108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 4108
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 15, 'TRANS': 481}
          Chain breaks: 3
  Time building chain proxies: 9.23, per 1000 atoms: 0.62
  Number of scatterers: 14906
  At special positions: 0
  Unit cell: (112.254, 127.08, 201.21, 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      51     16.00
     O    2780      8.00
     N    2679      7.00
     C    9396      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: 3.98
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3502

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      68.3% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 170
      removed outlier: 3.683A  pdb=" N   VAL B  69 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 170
    Processing helix  chain 'f' and resid 247 through 261
      removed outlier: 4.026A  pdb=" N   VAL f 259 " --> pdb=" O   GLU f 255 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS f 261 " --> pdb=" O   GLN f 257 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 270 through 293
      removed outlier: 3.565A  pdb=" N   GLU f 274 " --> pdb=" O   THR f 270 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 294 through 307
      removed outlier: 3.602A  pdb=" N   LEU f 298 " --> pdb=" O   SER f 294 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 309 through 319
      removed outlier: 4.061A  pdb=" N   THR f 313 " --> pdb=" O   ARG f 309 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 321 through 332
    Processing helix  chain 'f' and resid 332 through 337
    Processing helix  chain 'f' and resid 340 through 346
      removed outlier: 3.501A  pdb=" N   LEU f 344 " --> pdb=" O   PRO f 340 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER f 346 " --> pdb=" O   ASN f 342 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 349 through 364
    Processing helix  chain 'f' and resid 365 through 368
      removed outlier: 3.959A  pdb=" N   ARG f 368 " --> pdb=" O   ARG f 365 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'f' and resid 365 through 368'
    Processing helix  chain 'f' and resid 373 through 400
    Processing helix  chain 'f' and resid 405 through 439
      removed outlier: 3.571A  pdb=" N   PHE f 409 " --> pdb=" O   ALA f 405 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 455 through 483
      removed outlier: 4.602A  pdb=" N   LEU f 459 " --> pdb=" O   ALA f 455 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 513 through 533
      removed outlier: 4.022A  pdb=" N   ALA f 517 " --> pdb=" O   ASP f 513 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL f 533 " --> pdb=" O   ASN f 529 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 539 through 574
      removed outlier: 4.424A  pdb=" N   ARG f 559 " --> pdb=" O   GLU f 555 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   VAL f 560 " --> pdb=" O   ARG f 556 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   THR f 574 " --> pdb=" O   ASP f 570 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 577 through 586
    Processing helix  chain 'f' and resid 588 through 592
      removed outlier: 3.602A  pdb=" N   LEU f 591 " --> pdb=" O   PHE f 588 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   PHE f 592 " --> pdb=" O   ASN f 589 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'f' and resid 588 through 592'
    Processing helix  chain 'f' and resid 596 through 604
      removed outlier: 3.816A  pdb=" N   ALA f 600 " --> pdb=" O   HIS f 596 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 604 through 625
      removed outlier: 3.624A  pdb=" N   VAL f 625 " --> pdb=" O   ASP f 621 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 630 through 639
      removed outlier: 3.997A  pdb=" N   LYS f 634 " --> pdb=" O   SER f 630 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 642 through 670
    Processing helix  chain 'f' and resid 676 through 693
    Processing helix  chain 'f' and resid 695 through 710
      removed outlier: 3.529A  pdb=" N   PHE f 699 " --> pdb=" O   THR f 695 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 740 through 754
      removed outlier: 3.848A  pdb=" N   ILE f 744 " --> pdb=" O   LEU f 740 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 761 through 798
      Proline residue:  f 776  - end of helix
      removed outlier: 3.658A  pdb=" N   SER f 780 " --> pdb=" O   PRO f 776 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ARG f 798 " --> pdb=" O   LYS f 794 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 799 through 802
      removed outlier: 3.554A  pdb=" N   SER f 802 " --> pdb=" O   ASN f 799 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'f' and resid 799 through 802'
    Processing helix  chain 'f' and resid 805 through 820
    Processing helix  chain 'f' and resid 828 through 863
      removed outlier: 3.543A  pdb=" N   TYR f 832 " --> pdb=" O   LYS f 828 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL f 833 " --> pdb=" O   LEU f 829 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLN f 834 " --> pdb=" O   ASP f 830 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 870 through 891
      removed outlier: 3.641A  pdb=" N   PHE f 874 " --> pdb=" O   ASP f 870 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS f 891 " --> pdb=" O   ASP f 887 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 895 through 923
      removed outlier: 3.555A  pdb=" N   TRP f 899 " --> pdb=" O   ASN f 895 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU f 906 " --> pdb=" O   LYS f 902 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 986 through 995
      removed outlier: 4.110A  pdb=" N   VAL f 992 " --> pdb=" O   ALA f 988 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   VAL f 993 " --> pdb=" O   TRP f 989 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER f 995 " --> pdb=" O   MET f 991 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 1013 through 1018
    Processing helix  chain 'f' and resid 1030 through 1039
      removed outlier: 3.930A  pdb=" N   ALA f1039 " --> pdb=" O   GLU f1035 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 574 through 579
    Processing helix  chain 'h' and resid 583 through 608
    Processing helix  chain 'j' and resid 358 through 373
    Processing helix  chain 'm' and resid 178 through 198
    Processing helix  chain 'm' and resid 242 through 261
    Processing helix  chain 'm' and resid 270 through 293
    Processing helix  chain 'm' and resid 294 through 307
    Processing helix  chain 'm' and resid 309 through 318
      removed outlier: 3.699A  pdb=" N   THR m 313 " --> pdb=" O   ARG m 309 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 321 through 337
      removed outlier: 3.669A  pdb=" N   ALA m 325 " --> pdb=" O   GLY m 321 " (cutoff:3.500A)
      Proline residue:  m 334  - end of helix
    Processing helix  chain 'm' and resid 340 through 347
      removed outlier: 3.791A  pdb=" N   LEU m 344 " --> pdb=" O   PRO m 340 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 349 through 364
    Processing helix  chain 'm' and resid 365 through 369
      removed outlier: 4.084A  pdb=" N   ARG m 368 " --> pdb=" O   ARG m 365 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 373 through 400
    Processing helix  chain 'm' and resid 401 through 404
      removed outlier: 3.579A  pdb=" N   VAL m 404 " --> pdb=" O   LEU m 401 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 401 through 404'
    Processing helix  chain 'm' and resid 405 through 440
    Processing helix  chain 'm' and resid 456 through 484
      removed outlier: 3.719A  pdb=" N   GLN m 472 " --> pdb=" O   LYS m 468 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL m 479 " --> pdb=" O   GLN m 475 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 514 through 532
    Processing helix  chain 'm' and resid 539 through 569
    Processing helix  chain 'm' and resid 570 through 572
      No H-bonds generated for 'chain 'm' and resid 570 through 572'
    Processing helix  chain 'm' and resid 577 through 588
    Processing helix  chain 'm' and resid 589 through 593
      removed outlier: 3.896A  pdb=" N   VAL m 593 " --> pdb=" O   ALA m 590 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 594 through 601
      removed outlier: 3.531A  pdb=" N   ILE m 601 " --> pdb=" O   ILE m 597 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 602 through 623
      removed outlier: 3.836A  pdb=" N   THR m 606 " --> pdb=" O   ARG m 602 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLN m 607 " --> pdb=" O   GLU m 603 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 630 through 639
      removed outlier: 4.115A  pdb=" N   LYS m 634 " --> pdb=" O   SER m 630 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 642 through 670
    Processing helix  chain 'm' and resid 672 through 676
      removed outlier: 3.553A  pdb=" N   ASN m 675 " --> pdb=" O   GLY m 672 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 678 through 692
      removed outlier: 3.613A  pdb=" N   LEU m 682 " --> pdb=" O   GLU m 678 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LYS m 692 " --> pdb=" O   SER m 688 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 695 through 707
      removed outlier: 3.528A  pdb=" N   PHE m 699 " --> pdb=" O   THR m 695 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 746 through 754
    Processing helix  chain 'm' and resid 761 through 766
      removed outlier: 3.509A  pdb=" N   VAL m 765 " --> pdb=" O   PRO m 761 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASN m 766 " --> pdb=" O   LEU m 762 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'm' and resid 761 through 766'
    Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 723
    Processing sheet with id=AA2, first strand: chain 'h' and resid 239 through 245
      removed outlier: 5.835A  pdb=" N   LEU h 241 " --> pdb=" O   ASP h 572 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   ASP h 572 " --> pdb=" O   LEU h 241 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG h 243 " --> pdb=" O   ILE h 570 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'h' and resid 256 through 261
      removed outlier: 4.327A  pdb=" N   CYS h 258 " --> pdb=" O   SER h 272 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   VAL h 286 " --> pdb=" O   TYR h 273 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLY h 285 " --> pdb=" O   CYS h 305 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'h' and resid 309 through 314
    Processing sheet with id=AA5, first strand: chain 'h' and resid 358 through 365
      removed outlier: 3.878A  pdb=" N   CYS h 360 " --> pdb=" O   ILE h 375 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LYS h 380 " --> pdb=" O   SER h 376 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'h' and resid 408 through 412
    Processing sheet with id=AA7, first strand: chain 'h' and resid 453 through 458
      removed outlier: 3.647A  pdb=" N   SER h 475 " --> pdb=" O   THR h 479 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   THR h 479 " --> pdb=" O   SER h 475 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'h' and resid 501 through 506
      removed outlier: 4.062A  pdb=" N   ASP h 503 " --> pdb=" O   VAL h 517 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG h 522 " --> pdb=" O   ASP h 518 " (cutoff:3.500A)

    1018 hydrogen bonds defined for protein.
    3024 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: 4.61

  Time building geometry restraints manager: 4.60 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: 4928
        1.34 -     1.46: 3027
        1.46 -     1.58: 7133
        1.58 -     1.70: 0
        1.70 -     1.82: 89
  Bond restraints: 15177
  Sorted by residual:
  bond pdb=" CA  TYR h 500 "
       pdb=" C   TYR h 500 "
    ideal  model  delta    sigma   weight residual
    1.528  1.492  0.036 1.33e-02 5.65e+03 7.24e+00
  bond pdb=" CB  ASP m 436 "
       pdb=" CG  ASP m 436 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 2.50e-02 1.60e+03 4.29e+00
  bond pdb=" CB  ASP f 687 "
       pdb=" CG  ASP f 687 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 2.50e-02 1.60e+03 4.27e+00
  bond pdb=" CB  ASP B 113 "
       pdb=" CG  ASP B 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.568 -0.052 2.50e-02 1.60e+03 4.25e+00
  bond pdb=" CA  ASP h 496 "
       pdb=" C   ASP h 496 "
    ideal  model  delta    sigma   weight residual
    1.526  1.502  0.024 1.21e-02 6.83e+03 4.02e+00
  ... (remaining 15172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 20094
        3.21 -     6.43: 289
        6.43 -     9.64: 60
        9.64 -    12.85: 23
       12.85 -    16.06: 7
  Bond angle restraints: 20473
  Sorted by residual:
  angle pdb=" CA  GLN C 117 "
        pdb=" CB  GLN C 117 "
        pdb=" CG  GLN C 117 "
      ideal   model   delta    sigma   weight residual
     114.10  125.07  -10.97 2.00e+00 2.50e-01 3.01e+01
  angle pdb=" CB  MET j 364 "
        pdb=" CG  MET j 364 "
        pdb=" SD  MET j 364 "
      ideal   model   delta    sigma   weight residual
     112.70  128.58  -15.88 3.00e+00 1.11e-01 2.80e+01
  angle pdb=" CG1 ILE C 147 "
        pdb=" CB  ILE C 147 "
        pdb=" CG2 ILE C 147 "
      ideal   model   delta    sigma   weight residual
     110.70   95.30   15.40 3.00e+00 1.11e-01 2.63e+01
  angle pdb=" CB  LYS j 352 "
        pdb=" CG  LYS j 352 "
        pdb=" CD  LYS j 352 "
      ideal   model   delta    sigma   weight residual
     111.30  123.03  -11.73 2.30e+00 1.89e-01 2.60e+01
  angle pdb=" C   LYS m 337 "
        pdb=" N   ASP m 338 "
        pdb=" CA  ASP m 338 "
      ideal   model   delta    sigma   weight residual
     121.54  130.96   -9.42 1.91e+00 2.74e-01 2.43e+01
  ... (remaining 20468 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 7782
       18.01 -    36.01: 1114
       36.01 -    54.02: 314
       54.02 -    72.02: 68
       72.02 -    90.03: 26
  Dihedral angle restraints: 9304
    sinusoidal: 3948
      harmonic: 5356
  Sorted by residual:
  dihedral pdb=" CA  PHE f 339 "
           pdb=" C   PHE f 339 "
           pdb=" N   PRO f 340 "
           pdb=" CA  PRO f 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.45  -23.55     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ALA f 405 "
           pdb=" C   ALA f 405 "
           pdb=" N   TYR f 406 "
           pdb=" CA  TYR f 406 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.24  -21.76     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  TRP h 384 "
           pdb=" C   TRP h 384 "
           pdb=" N   SER h 385 "
           pdb=" CA  SER h 385 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 9301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 2193
       0.123 -    0.247: 53
       0.247 -    0.370: 5
       0.370 -    0.493: 0
       0.493 -    0.616: 1
  Chirality restraints: 2252
  Sorted by residual:
  chirality pdb=" CB  VAL f 404 "
            pdb=" CA  VAL f 404 "
            pdb=" CG1 VAL f 404 "
            pdb=" CG2 VAL f 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.01   -0.62 2.00e-01 2.50e+01 9.50e+00
  chirality pdb=" CG  LEU C 115 "
            pdb=" CB  LEU C 115 "
            pdb=" CD1 LEU C 115 "
            pdb=" CD2 LEU C 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  ILE C 147 "
            pdb=" CA  ILE C 147 "
            pdb=" CG1 ILE C 147 "
            pdb=" CG2 ILE C 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.98   -0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 2249 not shown)

  Planarity restraints: 2658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE m 339 "   -0.042 2.00e-02 2.50e+03   8.25e-02 6.80e+01
        pdb=" C   PHE m 339 "    0.143 2.00e-02 2.50e+03
        pdb=" O   PHE m 339 "   -0.054 2.00e-02 2.50e+03
        pdb=" N   PRO m 340 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE f 339 "   -0.041 2.00e-02 2.50e+03   8.15e-02 6.65e+01
        pdb=" C   PHE f 339 "    0.141 2.00e-02 2.50e+03
        pdb=" O   PHE f 339 "   -0.053 2.00e-02 2.50e+03
        pdb=" N   PRO f 340 "   -0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP f 546 "    0.026 2.00e-02 2.50e+03   2.06e-02 1.06e+01
        pdb=" CG  TRP f 546 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TRP f 546 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP f 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP f 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP f 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP f 546 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP f 546 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP f 546 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP f 546 "    0.009 2.00e-02 2.50e+03
  ... (remaining 2655 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.40: 20
        2.40 -     3.02: 7147
        3.02 -     3.65: 24186
        3.65 -     4.27: 32042
        4.27 -     4.90: 54092
  Nonbonded interactions: 117487
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN f 579 "
            pdb=" ND2 ASN h 497 "
     model   vdw
     1.770 3.200
  nonbonded pdb=" OG  SER h 257 "
            pdb=" O   MET h 310 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" NH2 ARG f1003 "
            pdb=" O   PHE m 623 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" O   LEU f1033 "
            pdb=" OG  SER f1036 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ASN f1021 "
            pdb=" OG1 THR f1024 "
     model   vdw
     2.320 3.040
  ... (remaining 117482 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  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:          0.620
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.670
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.070
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  15177  Z= 0.244
  Angle     :  1.033  16.063  20473  Z= 0.528
  Chirality :  0.052   0.616   2252
  Planarity :  0.007   0.082   2658
  Dihedral  : 18.623  90.028   5802
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.45 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 26.63 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.18), residues: 1794
  helix: -0.04 (0.13), residues: 1171
  sheet: -1.27 (0.39), residues: 166
  loop : -1.15 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP f 546 
 HIS   0.007   0.001   HIS B 168 
 PHE   0.046   0.003   PHE C 111 
 TYR   0.037   0.002   TYR B  94 
 ARG   0.011   0.001   ARG f1020 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10813 ( 1018)
  hydrogen bonds       : angle       5.21427 ( 3024)
  covalent geometry    : bond        0.00508 (15177)
  covalent geometry    : angle       1.03339 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 230
  time to evaluate  : 1.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 GLU cc_start: 0.8005 (pp20) cc_final: 0.7781 (pp20)
REVERT: B   94 TYR cc_start: 0.7749 (t80) cc_final: 0.7410 (t80)
REVERT: C  135 GLN cc_start: 0.8568 (pp30) cc_final: 0.8359 (pp30)
REVERT: f  246 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6960 (tm-30)
REVERT: h  388 MET cc_start: 0.7964 (mtp) cc_final: 0.7723 (mtp)
REVERT: j  365 LYS cc_start: 0.9188 (ttpp) cc_final: 0.8967 (ttpp)
  outliers start: 12
  outliers final: 2
  residues processed: 241
  average time/residue: 0.3194
  time to fit residues: 108.4093
Evaluate side-chains
  199 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 196
  time to evaluate  : 1.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain f residue  246 GLN
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  495 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 151 optimal weight:    0.5980
   chunk 135 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 91 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 162 optimal weight:    7.9990
   overall best weight:    1.3188

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B  87 ASN
C 162 ASN
** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
f 246 GLN
h 393 GLN
h 497 ASN
** h 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 637 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.112632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.080113 restraints weight = 30201.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.082497 restraints weight = 19641.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.083584 restraints weight = 12393.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15177  Z= 0.142
  Angle     :  0.552   9.099  20473  Z= 0.289
  Chirality :  0.039   0.187   2252
  Planarity :  0.004   0.050   2658
  Dihedral  :  4.348  32.324   2000
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 24.78 %
    Favored  : 72.44 %
  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:  1.13 (0.20), residues: 1794
  helix:  1.63 (0.15), residues: 1178
  sheet: -1.11 (0.39), residues: 171
  loop : -0.76 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP h 483 
 HIS   0.004   0.001   HIS B 165 
 PHE   0.024   0.002   PHE f 409 
 TYR   0.013   0.001   TYR f 427 
 ARG   0.006   0.000   ARG C 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04719 ( 1018)
  hydrogen bonds       : angle       3.86735 ( 3024)
  covalent geometry    : bond        0.00309 (15177)
  covalent geometry    : angle       0.55235 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 217
  time to evaluate  : 1.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 TYR cc_start: 0.7679 (t80) cc_final: 0.7250 (t80)
REVERT: C   84 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7316 (mtm110)
REVERT: C  135 GLN cc_start: 0.8554 (pp30) cc_final: 0.8277 (pp30)
REVERT: f  274 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7547 (tp30)
REVERT: f  640 ASP cc_start: 0.8432 (t0) cc_final: 0.8113 (t70)
REVERT: f  868 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7566 (ppp)
REVERT: h  388 MET cc_start: 0.7698 (mtp) cc_final: 0.7439 (mtp)
REVERT: h  595 ILE cc_start: 0.8801 (mt) cc_final: 0.8518 (mt)
REVERT: m  195 HIS cc_start: 0.7748 (m90) cc_final: 0.7494 (m90)
REVERT: m  336 MET cc_start: 0.7004 (mmm) cc_final: 0.6678 (mmm)
REVERT: m  467 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8333 (ttp-170)
  outliers start: 45
  outliers final: 26
  residues processed: 252
  average time/residue: 0.3125
  time to fit residues: 111.1069
Evaluate side-chains
  214 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  328 THR
Chi-restraints excluded: chain f residue  409 PHE
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  644 VAL
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  403 SER
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  398 THR
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  665 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 164 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 99 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 124 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 171 optimal weight:    0.9980
   chunk 128 optimal weight:    0.0070
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.7802

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B  87 ASN
f 257 GLN
f 363 HIS
h 274 ASN
h 393 GLN
h 548 ASN
** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 571 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.112504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.079855 restraints weight = 30104.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.082367 restraints weight = 18991.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082884 restraints weight = 13222.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  15177  Z= 0.118
  Angle     :  0.530   9.144  20473  Z= 0.274
  Chirality :  0.038   0.160   2252
  Planarity :  0.003   0.045   2658
  Dihedral  :  3.865  17.274   1994
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 25.77 %
    Favored  : 71.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.84 (0.20), residues: 1794
  helix:  2.22 (0.15), residues: 1181
  sheet: -1.10 (0.39), residues: 171
  loop : -0.55 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP h 483 
 HIS   0.004   0.001   HIS B 165 
 PHE   0.019   0.001   PHE f 409 
 TYR   0.011   0.001   TYR f 427 
 ARG   0.008   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04435 ( 1018)
  hydrogen bonds       : angle       3.66282 ( 3024)
  covalent geometry    : bond        0.00248 (15177)
  covalent geometry    : angle       0.52995 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 215
  time to evaluate  : 1.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   94 TYR cc_start: 0.7468 (t80) cc_final: 0.7191 (t80)
REVERT: C   84 ARG cc_start: 0.7768 (mtm110) cc_final: 0.7531 (mtm110)
REVERT: C  127 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7635 (pm20)
REVERT: f  274 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7388 (tp30)
REVERT: f  640 ASP cc_start: 0.8437 (t0) cc_final: 0.8193 (t70)
REVERT: f  868 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7526 (ppp)
REVERT: f 1010 TYR cc_start: 0.5515 (OUTLIER) cc_final: 0.4907 (p90)
REVERT: m  467 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8369 (ttp-170)
REVERT: m  521 GLU cc_start: 0.7850 (pp20) cc_final: 0.7363 (pp20)
  outliers start: 49
  outliers final: 20
  residues processed: 250
  average time/residue: 0.2911
  time to fit residues: 104.0328
Evaluate side-chains
  217 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  127 GLU
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  363 HIS
Chi-restraints excluded: chain f residue  434 LEU
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  816 ILE
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  403 SER
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0670
   chunk 71 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 151 optimal weight:    0.6980
   chunk 47 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 148 optimal weight:    3.9990
   chunk 153 optimal weight:    4.9990
   overall best weight:    1.5524

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B  87 ASN
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
f 769 HIS
h 393 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.111764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.078802 restraints weight = 30419.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.081038 restraints weight = 17469.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.082552 restraints weight = 12207.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15177  Z= 0.150
  Angle     :  0.534   8.409  20473  Z= 0.279
  Chirality :  0.039   0.154   2252
  Planarity :  0.003   0.041   2658
  Dihedral  :  3.832  18.235   1994
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 25.83 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.10 (0.20), residues: 1794
  helix:  2.45 (0.15), residues: 1180
  sheet: -1.05 (0.39), residues: 171
  loop : -0.49 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP h 483 
 HIS   0.010   0.001   HIS f 363 
 PHE   0.020   0.002   PHE f 409 
 TYR   0.013   0.001   TYR f 427 
 ARG   0.008   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04454 ( 1018)
  hydrogen bonds       : angle       3.67679 ( 3024)
  covalent geometry    : bond        0.00333 (15177)
  covalent geometry    : angle       0.53413 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 206
  time to evaluate  : 1.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  161 TYR cc_start: 0.5842 (t80) cc_final: 0.5441 (t80)
REVERT: f  274 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7361 (tp30)
REVERT: f  640 ASP cc_start: 0.8484 (t0) cc_final: 0.8243 (t70)
REVERT: f  868 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7586 (ppp)
REVERT: f 1010 TYR cc_start: 0.5230 (OUTLIER) cc_final: 0.4789 (p90)
REVERT: m  195 HIS cc_start: 0.7400 (m-70) cc_final: 0.7121 (m-70)
REVERT: m  354 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7900 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8352 (ttp-170)
REVERT: m  521 GLU cc_start: 0.7827 (pp20) cc_final: 0.7375 (pp20)
  outliers start: 61
  outliers final: 32
  residues processed: 254
  average time/residue: 0.3020
  time to fit residues: 108.9946
Evaluate side-chains
  226 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 1.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  328 THR
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  409 PHE
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  644 VAL
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  362 ASN
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  403 SER
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  442 ILE
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  504 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 170 optimal weight:    7.9990
   chunk 110 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0980
   chunk 109 optimal weight:    1.9990
   chunk 158 optimal weight:    5.9990
   chunk 172 optimal weight:    3.9990
   chunk 168 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 97 optimal weight:    0.8980
   chunk 144 optimal weight:    0.0980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
f 363 HIS
f 769 HIS
f1000 GLN
m 637 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.112413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.079511 restraints weight = 30526.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.081796 restraints weight = 17338.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.083380 restraints weight = 12018.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15177  Z= 0.127
  Angle     :  0.556  10.389  20473  Z= 0.286
  Chirality :  0.039   0.164   2252
  Planarity :  0.003   0.039   2658
  Dihedral  :  3.782  18.365   1994
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 26.26 %
    Favored  : 70.10 %
  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:  2.28 (0.20), residues: 1794
  helix:  2.57 (0.15), residues: 1181
  sheet: -1.00 (0.39), residues: 171
  loop : -0.37 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP h 483 
 HIS   0.007   0.001   HIS B 165 
 PHE   0.020   0.001   PHE f 409 
 TYR   0.013   0.001   TYR B  94 
 ARG   0.011   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04389 ( 1018)
  hydrogen bonds       : angle       3.63064 ( 3024)
  covalent geometry    : bond        0.00277 (15177)
  covalent geometry    : angle       0.55636 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 211
  time to evaluate  : 1.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 ARG cc_start: 0.7469 (ttm110) cc_final: 0.7157 (mtm110)
REVERT: C   84 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7431 (mtm110)
REVERT: C  103 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7537 (pp30)
REVERT: C  161 TYR cc_start: 0.5992 (t80) cc_final: 0.5722 (t80)
REVERT: f  274 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7476 (tp30)
REVERT: f  640 ASP cc_start: 0.8464 (t0) cc_final: 0.8226 (t70)
REVERT: f  755 TRP cc_start: 0.7965 (t60) cc_final: 0.6779 (t60)
REVERT: f  868 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7552 (ppp)
REVERT: f 1010 TYR cc_start: 0.5302 (OUTLIER) cc_final: 0.4768 (p90)
REVERT: m  336 MET cc_start: 0.6708 (mmm) cc_final: 0.6236 (mmm)
REVERT: m  354 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7886 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8359 (ttp-170)
REVERT: m  764 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6568 (mm)
  outliers start: 59
  outliers final: 31
  residues processed: 255
  average time/residue: 0.3298
  time to fit residues: 119.8330
Evaluate side-chains
  234 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 196
  time to evaluate  : 1.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  363 HIS
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  409 PHE
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  403 SER
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  504 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  370 THR
Chi-restraints excluded: chain m residue  398 THR
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 170 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 155 optimal weight:    0.8980
   chunk 142 optimal weight:    0.9990
   chunk 144 optimal weight:    3.9990
   chunk 125 optimal weight:    5.9990
   chunk 86 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
B  87 ASN
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
f 456 HIS
m 637 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.110861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.078017 restraints weight = 30716.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.080359 restraints weight = 19219.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.081548 restraints weight = 12307.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15177  Z= 0.165
  Angle     :  0.575   9.842  20473  Z= 0.297
  Chirality :  0.039   0.154   2252
  Planarity :  0.003   0.038   2658
  Dihedral  :  3.811  19.622   1994
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 26.70 %
    Favored  : 69.11 %
  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:  2.35 (0.20), residues: 1794
  helix:  2.63 (0.15), residues: 1183
  sheet: -1.05 (0.39), residues: 171
  loop : -0.35 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP h 483 
 HIS   0.014   0.001   HIS m 195 
 PHE   0.021   0.002   PHE h 476 
 TYR   0.015   0.001   TYR B  94 
 ARG   0.009   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 ( 1018)
  hydrogen bonds       : angle       3.66206 ( 3024)
  covalent geometry    : bond        0.00373 (15177)
  covalent geometry    : angle       0.57463 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 202
  time to evaluate  : 1.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   84 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7456 (mtm110)
REVERT: C  112 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7206 (tm-30)
REVERT: C  135 GLN cc_start: 0.8431 (pp30) cc_final: 0.8126 (pp30)
REVERT: C  147 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7051 (tp)
REVERT: C  161 TYR cc_start: 0.5962 (t80) cc_final: 0.5711 (t80)
REVERT: f  274 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7453 (tp30)
REVERT: f  640 ASP cc_start: 0.8479 (t0) cc_final: 0.8248 (t70)
REVERT: f  755 TRP cc_start: 0.7986 (t60) cc_final: 0.6742 (t60)
REVERT: f  868 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7573 (ppp)
REVERT: f  986 MET cc_start: 0.7404 (tmm) cc_final: 0.6931 (mmt)
REVERT: f 1010 TYR cc_start: 0.5618 (OUTLIER) cc_final: 0.5008 (p90)
REVERT: m  195 HIS cc_start: 0.7558 (m-70) cc_final: 0.7328 (m-70)
REVERT: m  336 MET cc_start: 0.6822 (mmm) cc_final: 0.6377 (mmm)
REVERT: m  354 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7943 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8419 (ttp-170)
REVERT: m  764 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6704 (mm)
  outliers start: 68
  outliers final: 44
  residues processed: 255
  average time/residue: 0.3105
  time to fit residues: 111.1215
Evaluate side-chains
  234 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 182
  time to evaluate  : 1.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  112 GLU
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  328 THR
Chi-restraints excluded: chain f residue  342 ASN
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  392 LEU
Chi-restraints excluded: chain f residue  409 PHE
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  816 ILE
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  851 LEU
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue  994 LEU
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  362 ASN
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  403 SER
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  442 ILE
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  465 VAL
Chi-restraints excluded: chain h residue  504 VAL
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  370 THR
Chi-restraints excluded: chain m residue  398 THR
Chi-restraints excluded: chain m residue  445 ASN
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 131 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0970
   chunk 155 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 143 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 GLN
C 103 GLN
f 769 HIS
h 274 ASN
m 453 ASN
m 465 GLN
m 620 HIS
m 637 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.112371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.081061 restraints weight = 30451.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.082335 restraints weight = 17692.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.082828 restraints weight = 12674.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15177  Z= 0.122
  Angle     :  0.572  11.228  20473  Z= 0.292
  Chirality :  0.038   0.167   2252
  Planarity :  0.003   0.038   2658
  Dihedral  :  3.743  18.154   1994
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 27.68 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.21), residues: 1794
  helix:  2.70 (0.15), residues: 1184
  sheet: -0.92 (0.40), residues: 172
  loop : -0.28 (0.32), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP h 384 
 HIS   0.012   0.001   HIS m 195 
 PHE   0.020   0.001   PHE f 409 
 TYR   0.022   0.001   TYR B  94 
 ARG   0.014   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04326 ( 1018)
  hydrogen bonds       : angle       3.57180 ( 3024)
  covalent geometry    : bond        0.00263 (15177)
  covalent geometry    : angle       0.57185 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 205
  time to evaluate  : 1.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 TYR cc_start: 0.7099 (t80) cc_final: 0.6688 (t80)
REVERT: C   84 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7484 (mtm110)
REVERT: C  103 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (pp30)
REVERT: C  112 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7156 (tm-30)
REVERT: C  147 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.6931 (tp)
REVERT: C  161 TYR cc_start: 0.5814 (t80) cc_final: 0.5561 (t80)
REVERT: f  274 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7362 (tp30)
REVERT: f  640 ASP cc_start: 0.8454 (t0) cc_final: 0.8245 (t70)
REVERT: f  755 TRP cc_start: 0.7972 (t60) cc_final: 0.6754 (t60)
REVERT: f  868 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7608 (ppp)
REVERT: f  986 MET cc_start: 0.7580 (tmm) cc_final: 0.7160 (mmt)
REVERT: f 1010 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.5010 (p90)
REVERT: m  354 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7967 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8398 (ttp-170)
REVERT: m  574 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7441 (t)
REVERT: m  754 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8157 (mtmm)
REVERT: m  764 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6678 (mm)
  outliers start: 55
  outliers final: 32
  residues processed: 248
  average time/residue: 0.3036
  time to fit residues: 106.9134
Evaluate side-chains
  234 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 192
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  112 GLU
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  392 LEU
Chi-restraints excluded: chain f residue  409 PHE
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  851 LEU
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  389 LEU
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  445 ASN
Chi-restraints excluded: chain m residue  453 ASN
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  574 THR
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 143 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 153 optimal weight:    8.9990
   chunk 127 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 99 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9980
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 355 GLN
** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 571 GLN
m 620 HIS
m 637 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.108974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.078287 restraints weight = 30653.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.078977 restraints weight = 17979.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.079277 restraints weight = 13397.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  15177  Z= 0.233
  Angle     :  0.647  11.986  20473  Z= 0.334
  Chirality :  0.042   0.164   2252
  Planarity :  0.004   0.049   2658
  Dihedral  :  3.935  22.007   1994
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 27.87 %
    Favored  : 67.88 %
  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:  2.34 (0.20), residues: 1794
  helix:  2.60 (0.15), residues: 1189
  sheet: -1.00 (0.39), residues: 169
  loop : -0.35 (0.32), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP h 483 
 HIS   0.013   0.001   HIS m 195 
 PHE   0.028   0.002   PHE h 476 
 TYR   0.027   0.002   TYR B  94 
 ARG   0.014   0.001   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04634 ( 1018)
  hydrogen bonds       : angle       3.80007 ( 3024)
  covalent geometry    : bond        0.00537 (15177)
  covalent geometry    : angle       0.64673 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 187
  time to evaluate  : 1.708 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 TYR cc_start: 0.7408 (t80) cc_final: 0.6938 (t80)
REVERT: C   84 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7424 (mtm110)
REVERT: C  103 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7990 (pp30)
REVERT: C  112 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7317 (tm-30)
REVERT: C  137 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8037 (tm-30)
REVERT: C  161 TYR cc_start: 0.5786 (t80) cc_final: 0.5545 (t80)
REVERT: f  274 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7387 (tp30)
REVERT: f  328 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8713 (p)
REVERT: f  640 ASP cc_start: 0.8497 (t0) cc_final: 0.8267 (t70)
REVERT: f  755 TRP cc_start: 0.8098 (t60) cc_final: 0.6863 (t60)
REVERT: f  818 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8789 (tm-30)
REVERT: f  868 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7692 (ppp)
REVERT: f 1010 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.5212 (p90)
REVERT: m  354 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7977 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8470 (ttp-170)
REVERT: m  574 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7769 (t)
REVERT: m  754 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8287 (mtmm)
REVERT: m  764 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6822 (mm)
  outliers start: 69
  outliers final: 43
  residues processed: 244
  average time/residue: 0.3175
  time to fit residues: 109.4833
Evaluate side-chains
  234 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 180
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  112 GLU
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  328 THR
Chi-restraints excluded: chain f residue  336 MET
Chi-restraints excluded: chain f residue  342 ASN
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  392 LEU
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  644 VAL
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  816 ILE
Chi-restraints excluded: chain f residue  818 GLU
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  851 LEU
Chi-restraints excluded: chain f residue  863 SER
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue  994 LEU
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  362 ASN
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  442 ILE
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  465 VAL
Chi-restraints excluded: chain h residue  504 VAL
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  196 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  370 THR
Chi-restraints excluded: chain m residue  398 THR
Chi-restraints excluded: chain m residue  445 ASN
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  571 GLN
Chi-restraints excluded: chain m residue  574 THR
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 155 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 176 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 175 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 153 optimal weight:    9.9990
   chunk 90 optimal weight:    0.0570
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
B  73 ASN
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 103 GLN
** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 355 GLN
m 453 ASN
m 620 HIS
m 637 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.081211 restraints weight = 30316.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.081826 restraints weight = 19647.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.082592 restraints weight = 14396.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15177  Z= 0.129
  Angle     :  0.609  12.177  20473  Z= 0.310
  Chirality :  0.039   0.183   2252
  Planarity :  0.003   0.046   2658
  Dihedral  :  3.821  18.473   1994
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 28.79 %
    Favored  : 67.88 %
  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:  2.50 (0.21), residues: 1794
  helix:  2.73 (0.15), residues: 1188
  sheet: -0.97 (0.40), residues: 172
  loop : -0.28 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP h 384 
 HIS   0.005   0.001   HIS f 363 
 PHE   0.032   0.001   PHE B 111 
 TYR   0.026   0.001   TYR B  94 
 ARG   0.014   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 ( 1018)
  hydrogen bonds       : angle       3.65952 ( 3024)
  covalent geometry    : bond        0.00280 (15177)
  covalent geometry    : angle       0.60910 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 196
  time to evaluate  : 1.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 TYR cc_start: 0.7566 (t80) cc_final: 0.7036 (t80)
REVERT: C   84 ARG cc_start: 0.7793 (mtm110) cc_final: 0.7503 (mtm110)
REVERT: C  103 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7627 (pp30)
REVERT: C  112 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7282 (tm-30)
REVERT: C  137 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8276 (pp20)
REVERT: C  161 TYR cc_start: 0.5669 (t80) cc_final: 0.5464 (t80)
REVERT: f  274 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7360 (tp30)
REVERT: f  339 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: f  755 TRP cc_start: 0.8021 (t60) cc_final: 0.6830 (t60)
REVERT: f  868 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7602 (ppp)
REVERT: f 1010 TYR cc_start: 0.5415 (OUTLIER) cc_final: 0.4947 (p90)
REVERT: m  336 MET cc_start: 0.6601 (mmm) cc_final: 0.6049 (mmm)
REVERT: m  354 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7911 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8438 (ttp-170)
REVERT: m  574 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7506 (t)
REVERT: m  754 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8349 (mtmm)
REVERT: m  764 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6715 (mm)
  outliers start: 54
  outliers final: 37
  residues processed: 240
  average time/residue: 0.3032
  time to fit residues: 102.8974
Evaluate side-chains
  235 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 188
  time to evaluate  : 1.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  112 GLU
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  336 MET
Chi-restraints excluded: chain f residue  339 PHE
Chi-restraints excluded: chain f residue  342 ASN
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  392 LEU
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  851 LEU
Chi-restraints excluded: chain f residue  857 ILE
Chi-restraints excluded: chain f residue  863 SER
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue  994 LEU
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  344 VAL
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  525 LEU
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  370 THR
Chi-restraints excluded: chain m residue  453 ASN
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  574 THR
Chi-restraints excluded: chain m residue  585 PHE
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 160 optimal weight:    0.1980
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 166 optimal weight:    0.3980
   chunk 115 optimal weight:    0.9990
   chunk 135 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
B 142 ASN
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 453 ASN
m 620 HIS
m 637 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.112213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.079579 restraints weight = 30501.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.082211 restraints weight = 17970.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.082730 restraints weight = 12354.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15177  Z= 0.131
  Angle     :  0.623  11.858  20473  Z= 0.319
  Chirality :  0.039   0.180   2252
  Planarity :  0.003   0.038   2658
  Dihedral  :  3.795  17.945   1994
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.98 %
    Favored  : 67.88 %
  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:  2.51 (0.21), residues: 1794
  helix:  2.72 (0.15), residues: 1187
  sheet: -0.88 (0.41), residues: 172
  loop : -0.26 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP h 384 
 HIS   0.005   0.001   HIS B 165 
 PHE   0.032   0.001   PHE B 111 
 TYR   0.040   0.001   TYR B  94 
 ARG   0.017   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04448 ( 1018)
  hydrogen bonds       : angle       3.65907 ( 3024)
  covalent geometry    : bond        0.00285 (15177)
  covalent geometry    : angle       0.62284 (20473)

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

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

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3588 Ramachandran restraints generated.
    1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 191
  time to evaluate  : 1.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  143 TYR cc_start: 0.7518 (t80) cc_final: 0.6463 (t80)
REVERT: C   84 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7488 (mtm110)
REVERT: C  103 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7558 (pp30)
REVERT: C  112 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7221 (tm-30)
REVERT: C  137 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8271 (pp20)
REVERT: f  274 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7387 (tp30)
REVERT: f  339 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7850 (t80)
REVERT: f  755 TRP cc_start: 0.8004 (t60) cc_final: 0.7377 (t60)
REVERT: f  868 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7573 (ppp)
REVERT: f 1010 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.4929 (p90)
REVERT: m  336 MET cc_start: 0.6762 (mmm) cc_final: 0.6372 (mmm)
REVERT: m  354 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7938 (ttp-110)
REVERT: m  467 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8468 (ttp-170)
REVERT: m  751 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7516 (ptt-90)
REVERT: m  754 LYS cc_start: 0.8777 (mtmm) cc_final: 0.8366 (mtmm)
REVERT: m  764 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6722 (mm)
  outliers start: 51
  outliers final: 38
  residues processed: 232
  average time/residue: 0.3011
  time to fit residues: 98.7296
Evaluate side-chains
  231 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 184
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain C residue  103 GLN
Chi-restraints excluded: chain C residue  112 GLU
Chi-restraints excluded: chain f residue  274 GLU
Chi-restraints excluded: chain f residue  336 MET
Chi-restraints excluded: chain f residue  339 PHE
Chi-restraints excluded: chain f residue  342 ASN
Chi-restraints excluded: chain f residue  388 LEU
Chi-restraints excluded: chain f residue  392 LEU
Chi-restraints excluded: chain f residue  419 VAL
Chi-restraints excluded: chain f residue  621 ASP
Chi-restraints excluded: chain f residue  685 ASP
Chi-restraints excluded: chain f residue  760 VAL
Chi-restraints excluded: chain f residue  795 VAL
Chi-restraints excluded: chain f residue  849 ASP
Chi-restraints excluded: chain f residue  851 LEU
Chi-restraints excluded: chain f residue  857 ILE
Chi-restraints excluded: chain f residue  863 SER
Chi-restraints excluded: chain f residue  868 MET
Chi-restraints excluded: chain f residue  904 ASP
Chi-restraints excluded: chain f residue  994 LEU
Chi-restraints excluded: chain f residue 1006 VAL
Chi-restraints excluded: chain f residue 1010 TYR
Chi-restraints excluded: chain h residue  342 THR
Chi-restraints excluded: chain h residue  381 ILE
Chi-restraints excluded: chain h residue  406 VAL
Chi-restraints excluded: chain h residue  415 VAL
Chi-restraints excluded: chain h residue  456 ILE
Chi-restraints excluded: chain h residue  525 LEU
Chi-restraints excluded: chain h residue  550 VAL
Chi-restraints excluded: chain j residue  349 VAL
Chi-restraints excluded: chain m residue  189 LEU
Chi-restraints excluded: chain m residue  200 ILE
Chi-restraints excluded: chain m residue  249 VAL
Chi-restraints excluded: chain m residue  251 ARG
Chi-restraints excluded: chain m residue  263 ASP
Chi-restraints excluded: chain m residue  304 LEU
Chi-restraints excluded: chain m residue  341 LEU
Chi-restraints excluded: chain m residue  354 ARG
Chi-restraints excluded: chain m residue  370 THR
Chi-restraints excluded: chain m residue  453 ASN
Chi-restraints excluded: chain m residue  467 ARG
Chi-restraints excluded: chain m residue  585 PHE
Chi-restraints excluded: chain m residue  665 VAL
Chi-restraints excluded: chain m residue  706 VAL
Chi-restraints excluded: chain m residue  764 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 179
   random chunks:
   chunk 150 optimal weight:    3.9990
   chunk 168 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 133 optimal weight:    0.0970
   chunk 14 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** m 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
m 453 ASN
m 620 HIS
m 637 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.111155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.078412 restraints weight = 30351.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.080837 restraints weight = 19384.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.081409 restraints weight = 13858.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.164  15177  Z= 0.166
  Angle     :  0.816  58.240  20473  Z= 0.450
  Chirality :  0.040   0.270   2252
  Planarity :  0.003   0.055   2658
  Dihedral  :  3.859  34.132   1994
  Min Nonbonded Distance : 1.652

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 29.16 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  2.49 (0.21), residues: 1794
  helix:  2.70 (0.15), residues: 1187
  sheet: -0.89 (0.40), residues: 172
  loop : -0.27 (0.32), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP h 384 
 HIS   0.004   0.001   HIS f 363 
 PHE   0.028   0.001   PHE B 111 
 TYR   0.039   0.001   TYR B  94 
 ARG   0.018   0.000   ARG B 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 ( 1018)
  hydrogen bonds       : angle       3.66152 ( 3024)
  covalent geometry    : bond        0.00360 (15177)
  covalent geometry    : angle       0.81567 (20473)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4823.55 seconds
wall clock time: 85 minutes 24.00 seconds (5124.00 seconds total)