Starting phenix.real_space_refine
on Fri Jul  3 07:47:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8s_61240/07_2026/9j8s_61240.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=  -0.003 sd=   0.143
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      42      5.16       5
     C    8188      2.51       5
     N    2144      2.21       5
     O    2098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12474
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 802, 6158
          Classifications: {'peptide': 802}
          Link IDs: {'PTRANS': 43, 'TRANS': 758}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 79
          Unusual residues: {'PGT': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PGT:plan-1': 2, 'PGT:plan-2': 2}
          Unresolved non-hydrogen planarities: 14
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.03, per 1000 atoms: 0.48
  Number of scatterers: 12474
  At special positions: 0
  Unit cell: (93.09, 129.47, 120.91, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P       2     15.00
     O    2098      8.00
     N    2144      7.00
     C    8188      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 644.9 milliseconds
  

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2976

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 6 sheets defined
      67.5% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 56
    Processing helix  chain 'A' and resid 60 through 71
      removed outlier: 3.696A  pdb=" N   VAL A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 102
      removed outlier: 3.657A  pdb=" N   ALA A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLY A  92 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR A  93 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 125
      removed outlier: 3.658A  pdb=" N   ALA A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
    Processing helix  chain 'A' and resid 145 through 174
      removed outlier: 3.946A  pdb=" N   LEU A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      Proline residue:  A 165  - end of helix
      removed outlier: 3.636A  pdb=" N   CYS A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 186 through 211
      removed outlier: 3.678A  pdb=" N   HIS A 211 " --> pdb=" O   PHE A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 262
      removed outlier: 3.624A  pdb=" N   LEU A 258 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 261 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 285
    Processing helix  chain 'A' and resid 292 through 302
    Processing helix  chain 'A' and resid 308 through 323
    Processing helix  chain 'A' and resid 323 through 345
    Processing helix  chain 'A' and resid 356 through 377
    Processing helix  chain 'A' and resid 380 through 391
      removed outlier: 4.103A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LEU A 390 " --> pdb=" O   HIS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 3.557A  pdb=" N   ILE A 396 " --> pdb=" O   PRO A 392 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASP A 397 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA A 414 " --> pdb=" O   CYS A 410 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLN A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLY A 416 " --> pdb=" O   LEU A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 441
      removed outlier: 3.722A  pdb=" N   LEU A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 462
    Processing helix  chain 'A' and resid 471 through 475
    Processing helix  chain 'A' and resid 478 through 500
    Processing helix  chain 'A' and resid 506 through 510
      removed outlier: 3.748A  pdb=" N   TRP A 510 " --> pdb=" O   ASN A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 542
    Processing helix  chain 'A' and resid 553 through 566
    Processing helix  chain 'A' and resid 570 through 576
      removed outlier: 3.680A  pdb=" N   LEU A 574 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 628
      removed outlier: 3.643A  pdb=" N   GLU A 616 " --> pdb=" O   MET A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 649
      removed outlier: 3.569A  pdb=" N   ILE A 648 " --> pdb=" O   PHE A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 689
    Processing helix  chain 'A' and resid 701 through 715
    Processing helix  chain 'A' and resid 729 through 734
    Processing helix  chain 'A' and resid 776 through 793
    Processing helix  chain 'A' and resid 835 through 842
    Processing helix  chain 'A' and resid 861 through 870
    Processing helix  chain 'B' and resid 34 through 56
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 3.696A  pdb=" N   VAL B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 102
      removed outlier: 3.657A  pdb=" N   ALA B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B  91 " --> pdb=" O   PHE B  87 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   GLY B  92 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR B  93 " --> pdb=" O   ILE B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 125
      removed outlier: 3.658A  pdb=" N   ALA B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 140
    Processing helix  chain 'B' and resid 145 through 174
      removed outlier: 3.946A  pdb=" N   LEU B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      Proline residue:  B 165  - end of helix
      removed outlier: 3.635A  pdb=" N   CYS B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 184
    Processing helix  chain 'B' and resid 186 through 211
      removed outlier: 3.678A  pdb=" N   HIS B 211 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 262
      removed outlier: 3.624A  pdb=" N   LEU B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 261 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 285
    Processing helix  chain 'B' and resid 292 through 302
    Processing helix  chain 'B' and resid 308 through 323
    Processing helix  chain 'B' and resid 323 through 345
    Processing helix  chain 'B' and resid 356 through 377
    Processing helix  chain 'B' and resid 380 through 391
      removed outlier: 4.103A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LEU B 390 " --> pdb=" O   HIS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 419
      removed outlier: 3.557A  pdb=" N   ILE B 396 " --> pdb=" O   PRO B 392 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASP B 397 " --> pdb=" O   HIS B 393 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ALA B 414 " --> pdb=" O   CYS B 410 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLN B 415 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   GLY B 416 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 441
      removed outlier: 3.722A  pdb=" N   LEU B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU B 440 " --> pdb=" O   ALA B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 462
    Processing helix  chain 'B' and resid 471 through 475
    Processing helix  chain 'B' and resid 478 through 500
    Processing helix  chain 'B' and resid 506 through 510
      removed outlier: 3.748A  pdb=" N   TRP B 510 " --> pdb=" O   ASN B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 542
    Processing helix  chain 'B' and resid 553 through 566
    Processing helix  chain 'B' and resid 570 through 576
      removed outlier: 3.681A  pdb=" N   LEU B 574 " --> pdb=" O   ASP B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 628
      removed outlier: 3.643A  pdb=" N   GLU B 616 " --> pdb=" O   MET B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 649
      removed outlier: 3.569A  pdb=" N   ILE B 648 " --> pdb=" O   PHE B 644 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 689
    Processing helix  chain 'B' and resid 701 through 715
    Processing helix  chain 'B' and resid 729 through 734
    Processing helix  chain 'B' and resid 776 through 793
    Processing helix  chain 'B' and resid 835 through 842
    Processing helix  chain 'B' and resid 861 through 870
    Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 226
    Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584
      removed outlier: 6.241A  pdb=" N   MET A 601 " --> pdb=" O   VAL A 633 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   TYR A 635 " --> pdb=" O   MET A 601 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ALA A 603 " --> pdb=" O   TYR A 635 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL A 637 " --> pdb=" O   ALA A 603 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   TYR A 851 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   LEU A 852 " --> pdb=" O   LYS A 654 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   LYS A 654 " --> pdb=" O   LEU A 852 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   VAL A 854 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   ALA A 652 " --> pdb=" O   VAL A 854 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY A 800 " --> pdb=" O   ALA A 659 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL A 661 " --> pdb=" O   SER A 798 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   SER A 798 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA A 762 " --> pdb=" O   SER A 798 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   GLY A 800 " --> pdb=" O   ALA A 762 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 690 through 695
      removed outlier: 4.163A  pdb=" N   ARG A 737 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA A 749 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   HIS A 743 " --> pdb=" O   PRO A 747 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 226
    Processing sheet with id=AA5, first strand: chain 'B' and resid 581 through 584
      removed outlier: 6.241A  pdb=" N   MET B 601 " --> pdb=" O   VAL B 633 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   TYR B 635 " --> pdb=" O   MET B 601 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   ALA B 603 " --> pdb=" O   TYR B 635 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL B 637 " --> pdb=" O   ALA B 603 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   TYR B 851 " --> pdb=" O   GLN B 636 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   LEU B 852 " --> pdb=" O   LYS B 654 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   LYS B 654 " --> pdb=" O   LEU B 852 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   VAL B 854 " --> pdb=" O   ALA B 652 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   ALA B 652 " --> pdb=" O   VAL B 854 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 800 " --> pdb=" O   ALA B 659 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   VAL B 661 " --> pdb=" O   SER B 798 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   SER B 798 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA B 762 " --> pdb=" O   SER B 798 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   GLY B 800 " --> pdb=" O   ALA B 762 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 690 through 695
      removed outlier: 4.163A  pdb=" N   ARG B 737 " --> pdb=" O   LEU B 753 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ALA B 749 " --> pdb=" O   VAL B 741 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   HIS B 743 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)

    849 hydrogen bonds defined for protein.
    2487 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.63

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2313
        1.33 -     1.45: 3059
        1.45 -     1.57: 7306
        1.57 -     1.70: 4
        1.70 -     1.82: 68
  Bond restraints: 12750
  Sorted by residual:
  bond pdb=" C1  PGT A 903 "
       pdb=" O3P PGT A 903 "
    ideal  model  delta    sigma   weight residual
    1.408  1.460 -0.052 2.00e-02 2.50e+03 6.77e+00
  bond pdb=" C1  PGT B 903 "
       pdb=" O3P PGT B 903 "
    ideal  model  delta    sigma   weight residual
    1.408  1.460 -0.052 2.00e-02 2.50e+03 6.77e+00
  bond pdb=" CA  SER B 219 "
       pdb=" CB  SER B 219 "
    ideal  model  delta    sigma   weight residual
    1.536  1.509  0.028 1.23e-02 6.61e+03 5.00e+00
  bond pdb=" CA  SER A 219 "
       pdb=" CB  SER A 219 "
    ideal  model  delta    sigma   weight residual
    1.536  1.509  0.028 1.23e-02 6.61e+03 5.00e+00
  bond pdb=" CA  SER A 404 "
       pdb=" CB  SER A 404 "
    ideal  model  delta    sigma   weight residual
    1.529  1.493  0.036 1.62e-02 3.81e+03 4.98e+00
  ... (remaining 12745 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 16748
        2.26 -     4.52: 558
        4.52 -     6.78: 4
        6.78 -     9.04: 0
        9.04 -    11.30: 2
  Bond angle restraints: 17312
  Sorted by residual:
  angle pdb=" O3P PGT A 903 "
        pdb=" P   PGT A 903 "
        pdb=" O4P PGT A 903 "
      ideal   model   delta    sigma   weight residual
      92.82  104.12  -11.30 3.00e+00 1.11e-01 1.42e+01
  angle pdb=" O3P PGT B 903 "
        pdb=" P   PGT B 903 "
        pdb=" O4P PGT B 903 "
      ideal   model   delta    sigma   weight residual
      92.82  104.09  -11.27 3.00e+00 1.11e-01 1.41e+01
  angle pdb=" N   PRO B 469 "
        pdb=" CA  PRO B 469 "
        pdb=" CB  PRO B 469 "
      ideal   model   delta    sigma   weight residual
     102.81  100.44    2.37 6.70e-01 2.23e+00 1.25e+01
  angle pdb=" N   PRO A 469 "
        pdb=" CA  PRO A 469 "
        pdb=" CB  PRO A 469 "
      ideal   model   delta    sigma   weight residual
     102.81  100.44    2.37 6.70e-01 2.23e+00 1.25e+01
  angle pdb=" N   ASP B 589 "
        pdb=" CA  ASP B 589 "
        pdb=" C   ASP B 589 "
      ideal   model   delta    sigma   weight residual
     113.55  109.37    4.18 1.26e+00 6.30e-01 1.10e+01
  ... (remaining 17307 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.18: 6706
       15.18 -    30.35: 674
       30.35 -    45.53: 156
       45.53 -    60.70: 44
       60.70 -    75.88: 20
  Dihedral angle restraints: 7600
    sinusoidal: 2988
      harmonic: 4612
  Sorted by residual:
  dihedral pdb=" CA  GLY B 354 "
           pdb=" C   GLY B 354 "
           pdb=" N   PHE B 355 "
           pdb=" CA  PHE B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.04  -18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  GLY A 354 "
           pdb=" C   GLY A 354 "
           pdb=" N   PHE A 355 "
           pdb=" CA  PHE A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.04  -18.96     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  ALA B 603 "
           pdb=" C   ALA B 603 "
           pdb=" N   LEU B 604 "
           pdb=" CA  LEU B 604 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.01  -17.99     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 7597 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1257
       0.038 -    0.077: 440
       0.077 -    0.115: 263
       0.115 -    0.153: 60
       0.153 -    0.192: 4
  Chirality restraints: 2024
  Sorted by residual:
  chirality pdb=" CB  VAL A 124 "
            pdb=" CA  VAL A 124 "
            pdb=" CG1 VAL A 124 "
            pdb=" CG2 VAL A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CB  VAL B 124 "
            pdb=" CA  VAL B 124 "
            pdb=" CG1 VAL B 124 "
            pdb=" CG2 VAL B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.12e-01
  chirality pdb=" CA  PRO A 643 "
            pdb=" N   PRO A 643 "
            pdb=" C   PRO A 643 "
            pdb=" CB  PRO A 643 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 2021 not shown)

  Planarity restraints: 2170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 619 "   -0.022 2.00e-02 2.50e+03   1.25e-02 3.90e+00
        pdb=" CG  TRP A 619 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 619 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 619 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 619 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 619 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 619 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 619 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 619 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 619 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 619 "    0.022 2.00e-02 2.50e+03   1.25e-02 3.88e+00
        pdb=" CG  TRP B 619 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 619 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 619 "   -0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 619 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 619 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 619 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 619 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 619 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 619 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 645 "    0.026 2.00e-02 2.50e+03   1.32e-02 3.50e+00
        pdb=" CG  TYR B 645 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 645 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 645 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 645 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 645 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 645 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B 645 "    0.015 2.00e-02 2.50e+03
  ... (remaining 2167 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 3574
        2.83 -     3.34: 12106
        3.34 -     3.86: 20225
        3.86 -     4.38: 23098
        4.38 -     4.90: 39674
  Nonbonded interactions: 98677
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 282 "
            pdb=" OG  SER B 285 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   GLY A 282 "
            pdb=" OG  SER A 285 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   PHE B 723 "
            pdb=" OG  SER B 724 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   PHE A 723 "
            pdb=" OG  SER A 724 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" N   GLU B 448 "
            pdb=" OE1 GLU B 448 "
     model   vdw
     2.395 3.120
  ... (remaining 98672 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.170
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
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      :  0.007   0.052  12750  Z= 0.472
  Angle     :  1.033  11.296  17312  Z= 0.745
  Chirality :  0.050   0.192   2024
  Planarity :  0.006   0.063   2170
  Dihedral  : 13.799  75.875   4624
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.52 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.48 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.18), residues: 1592
  helix: -0.39 (0.14), residues: 1038
  sheet: -0.20 (0.38), residues: 160
  loop : -1.73 (0.29), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 468 
 TYR   0.026   0.003   TYR B 645 
 PHE   0.029   0.003   PHE A 466 
 TRP   0.022   0.003   TRP A 619 
 HIS   0.009   0.001   HIS B 386 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00704 /  0.47 (12750)
  covalent geometry    : angle       1.03341 /  0.74 (17312)
  hydrogen bonds       : bond        0.15556 / 10.43 (  849)
  hydrogen bonds       : angle       6.65771 /  4.85 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 168
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 TYR cc_start: 0.6886 (t80) cc_final: 0.6537 (t80)
REVERT: A  178 ASP cc_start: 0.7573 (m-30) cc_final: 0.7293 (p0)
REVERT: A  464 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7025 (mmm160)
REVERT: A  530 CYS cc_start: 0.7489 (m) cc_final: 0.7230 (t)
REVERT: A  551 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6788 (mp0)
REVERT: A  596 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7334 (ttt90)
REVERT: B  136 TYR cc_start: 0.6886 (t80) cc_final: 0.6539 (t80)
REVERT: B  178 ASP cc_start: 0.7572 (m-30) cc_final: 0.7292 (p0)
REVERT: B  464 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7025 (mmm160)
REVERT: B  530 CYS cc_start: 0.7489 (m) cc_final: 0.7231 (t)
REVERT: B  551 GLU cc_start: 0.7791 (mm-30) cc_final: 0.6791 (mp0)
REVERT: B  596 ARG cc_start: 0.7807 (ttt180) cc_final: 0.7332 (ttt90)
  outliers start: 2
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1331
  time to fit residues: 30.5857
Evaluate side-chains
  128 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0030
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.8992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.177601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.140314 restraints weight = 13610.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138831 restraints weight = 21078.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.141470 restraints weight = 17539.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139582 restraints weight = 11803.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.140096 restraints weight = 10887.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  12750  Z= 0.153
  Angle     :  0.571   7.694  17312  Z= 0.279
  Chirality :  0.037   0.209   2024
  Planarity :  0.004   0.034   2170
  Dihedral  :  5.554  45.456   1866
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.24 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.21), residues: 1592
  helix:  1.99 (0.15), residues: 1048
  sheet:  0.21 (0.38), residues: 162
  loop : -1.12 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 471 
 TYR   0.017   0.002   TYR A 680 
 PHE   0.011   0.001   PHE A  87 
 TRP   0.009   0.001   TRP B 446 
 HIS   0.004   0.001   HIS B 400 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 (12750)
  covalent geometry    : angle       0.57134 /  0.28 (17312)
  hydrogen bonds       : bond        0.04346 /  2.96 (  849)
  hydrogen bonds       : angle       4.22445 /  3.04 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7598 (mtt) cc_final: 0.7318 (mtt)
REVERT: B  601 MET cc_start: 0.7591 (mtt) cc_final: 0.7312 (mtt)
  outliers start: 26
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1217
  time to fit residues: 26.5662
Evaluate side-chains
  134 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  765 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 120 optimal weight:    0.6980
   chunk 154 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0570
   chunk 121 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0040
   chunk 67 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0870
   overall best weight:    0.2688

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 400 HIS
B 400 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.182635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144416 restraints weight = 13590.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143186 restraints weight = 19872.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.145093 restraints weight = 17949.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144720 restraints weight = 13005.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.145188 restraints weight = 11877.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.072  12750  Z= 0.105
  Angle     :  0.505   5.764  17312  Z= 0.244
  Chirality :  0.035   0.221   2024
  Planarity :  0.004   0.038   2170
  Dihedral  :  5.155  38.500   1866
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 10.24 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.21), residues: 1592
  helix:  2.48 (0.15), residues: 1052
  sheet:  0.33 (0.38), residues: 162
  loop : -0.75 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 684 
 TYR   0.017   0.001   TYR A 680 
 PHE   0.012   0.001   PHE B  87 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.004   0.000   HIS A 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 (12750)
  covalent geometry    : angle       0.50455 /  0.24 (17312)
  hydrogen bonds       : bond        0.03503 /  2.36 (  849)
  hydrogen bonds       : angle       3.83272 /  2.75 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 136
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7687 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8132 (tppt)
REVERT: B  684 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7688 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8135 (tppt)
  outliers start: 36
  outliers final: 16
  residues processed: 160
  average time/residue: 0.1132
  time to fit residues: 25.7622
Evaluate side-chains
  134 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 133 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 144 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 90 optimal weight:    0.4980
   chunk 86 optimal weight:    0.8980
   chunk 140 optimal weight:    0.6980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.175407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.137094 restraints weight = 13387.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.136147 restraints weight = 18596.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.137619 restraints weight = 16245.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.137384 restraints weight = 12999.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.137479 restraints weight = 12220.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12750  Z= 0.128
  Angle     :  0.513   5.432  17312  Z= 0.247
  Chirality :  0.036   0.208   2024
  Planarity :  0.004   0.039   2170
  Dihedral  :  5.298  44.167   1866
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.20 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.21), residues: 1592
  helix:  2.50 (0.15), residues: 1052
  sheet:  0.56 (0.39), residues: 162
  loop : -0.67 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 521 
 TYR   0.017   0.001   TYR A 680 
 PHE   0.022   0.001   PHE B 839 
 TRP   0.008   0.001   TRP B 446 
 HIS   0.003   0.001   HIS B 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.13 (12750)
  covalent geometry    : angle       0.51278 /  0.25 (17312)
  hydrogen bonds       : bond        0.03640 /  2.46 (  849)
  hydrogen bonds       : angle       3.84268 /  2.76 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7566 (mtt) cc_final: 0.7316 (mtt)
REVERT: A  706 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8119 (tppt)
REVERT: B  601 MET cc_start: 0.7523 (mtt) cc_final: 0.7281 (mtt)
REVERT: B  706 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8121 (tppt)
  outliers start: 34
  outliers final: 18
  residues processed: 148
  average time/residue: 0.1102
  time to fit residues: 23.5298
Evaluate side-chains
  138 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 104 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 159 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 153 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 507 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.177255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138524 restraints weight = 13649.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.137253 restraints weight = 21009.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139674 restraints weight = 18076.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138490 restraints weight = 13145.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138815 restraints weight = 12641.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12750  Z= 0.135
  Angle     :  0.522   5.447  17312  Z= 0.252
  Chirality :  0.036   0.250   2024
  Planarity :  0.004   0.038   2170
  Dihedral  :  5.395  45.812   1866
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 10.56 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.21), residues: 1592
  helix:  2.49 (0.15), residues: 1050
  sheet:  0.65 (0.39), residues: 162
  loop : -0.65 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 684 
 TYR   0.015   0.001   TYR B 680 
 PHE   0.023   0.001   PHE B 839 
 TRP   0.009   0.001   TRP B 446 
 HIS   0.003   0.001   HIS A 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 (12750)
  covalent geometry    : angle       0.52195 /  0.25 (17312)
  hydrogen bonds       : bond        0.03659 /  2.48 (  849)
  hydrogen bonds       : angle       3.82728 /  2.76 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 127
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7593 (mtt) cc_final: 0.7297 (mtt)
REVERT: A  602 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8156 (mm)
REVERT: A  684 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7494 (ttm-80)
REVERT: B  601 MET cc_start: 0.7584 (mtt) cc_final: 0.7286 (mtt)
REVERT: B  602 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8147 (mm)
REVERT: B  684 ARG cc_start: 0.8043 (ttp-110) cc_final: 0.7494 (ttm-80)
  outliers start: 53
  outliers final: 27
  residues processed: 169
  average time/residue: 0.0943
  time to fit residues: 23.4492
Evaluate side-chains
  151 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  507 ASN
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 132 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 148 optimal weight:    0.0470
   chunk 153 optimal weight:    7.9990
   chunk 112 optimal weight:    0.0070
   overall best weight:    0.4896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 507 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.177104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139491 restraints weight = 13620.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.138180 restraints weight = 19543.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.139250 restraints weight = 17686.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.138776 restraints weight = 14220.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.139533 restraints weight = 13090.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12750  Z= 0.111
  Angle     :  0.508   5.427  17312  Z= 0.245
  Chirality :  0.035   0.238   2024
  Planarity :  0.004   0.038   2170
  Dihedral  :  5.297  44.163   1866
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 10.80 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.21), residues: 1592
  helix:  2.56 (0.16), residues: 1052
  sheet:  0.73 (0.39), residues: 162
  loop : -0.60 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 524 
 TYR   0.014   0.001   TYR B 680 
 PHE   0.023   0.001   PHE B 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.002   0.000   HIS A 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 (12750)
  covalent geometry    : angle       0.50843 /  0.25 (17312)
  hydrogen bonds       : bond        0.03388 /  2.29 (  849)
  hydrogen bonds       : angle       3.77599 /  2.72 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 VAL cc_start: 0.8178 (t) cc_final: 0.7895 (p)
REVERT: A  601 MET cc_start: 0.7607 (mtt) cc_final: 0.7294 (mtt)
REVERT: A  684 ARG cc_start: 0.8025 (ttp-110) cc_final: 0.7537 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8450 (mtmm) cc_final: 0.7916 (tppt)
REVERT: B  408 VAL cc_start: 0.8179 (t) cc_final: 0.7903 (p)
REVERT: B  601 MET cc_start: 0.7656 (mtt) cc_final: 0.7353 (mtt)
REVERT: B  684 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7539 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8463 (mtmm) cc_final: 0.7922 (tppt)
  outliers start: 41
  outliers final: 25
  residues processed: 165
  average time/residue: 0.0960
  time to fit residues: 23.2902
Evaluate side-chains
  149 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 99 optimal weight:    9.9990
   chunk 113 optimal weight:    0.5980
   chunk 86 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0970
   chunk 105 optimal weight:    0.2980
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.3978

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.181596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.144394 restraints weight = 13525.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.143209 restraints weight = 19367.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.143745 restraints weight = 16376.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.143949 restraints weight = 14422.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144474 restraints weight = 12536.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  12750  Z= 0.107
  Angle     :  0.510   7.347  17312  Z= 0.247
  Chirality :  0.036   0.265   2024
  Planarity :  0.004   0.039   2170
  Dihedral  :  5.208  43.776   1866
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.92 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.21), residues: 1592
  helix:  2.58 (0.16), residues: 1052
  sheet:  0.74 (0.39), residues: 162
  loop : -0.58 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 464 
 TYR   0.012   0.001   TYR B 680 
 PHE   0.024   0.001   PHE A 839 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.003   0.000   HIS A 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 (12750)
  covalent geometry    : angle       0.50998 /  0.25 (17312)
  hydrogen bonds       : bond        0.03307 /  2.24 (  849)
  hydrogen bonds       : angle       3.72530 /  2.69 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 129
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 VAL cc_start: 0.8124 (t) cc_final: 0.7872 (p)
REVERT: A  601 MET cc_start: 0.7681 (mtt) cc_final: 0.7355 (mtt)
REVERT: A  684 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7638 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8059 (tppt)
REVERT: B  408 VAL cc_start: 0.8134 (t) cc_final: 0.7882 (p)
REVERT: B  601 MET cc_start: 0.7676 (mtt) cc_final: 0.7352 (mtt)
REVERT: B  684 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7643 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8061 (tppt)
  outliers start: 34
  outliers final: 26
  residues processed: 155
  average time/residue: 0.1130
  time to fit residues: 25.6807
Evaluate side-chains
  148 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  792 GLN
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  792 GLN
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 159 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0670
   chunk 44 optimal weight:    0.7980
   chunk 111 optimal weight:    0.0170
   chunk 147 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0070
   chunk 155 optimal weight:    3.9990
   overall best weight:    0.7776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 734 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.179993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.141967 restraints weight = 13553.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140469 restraints weight = 20294.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142492 restraints weight = 18067.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.142029 restraints weight = 13770.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.142745 restraints weight = 13025.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12750  Z= 0.135
  Angle     :  0.541   6.840  17312  Z= 0.259
  Chirality :  0.037   0.274   2024
  Planarity :  0.004   0.040   2170
  Dihedral  :  5.393  46.399   1866
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 12.80 %
    Favored  : 84.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.22), residues: 1592
  helix:  2.45 (0.16), residues: 1052
  sheet:  0.75 (0.40), residues: 162
  loop : -0.61 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 464 
 TYR   0.015   0.002   TYR B 136 
 PHE   0.026   0.001   PHE A 839 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.002   0.000   HIS B 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.13 (12750)
  covalent geometry    : angle       0.54148 /  0.26 (17312)
  hydrogen bonds       : bond        0.03600 /  2.44 (  849)
  hydrogen bonds       : angle       3.83105 /  2.76 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7608 (mtt) cc_final: 0.7281 (mtt)
REVERT: A  684 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7676 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8023 (tppt)
REVERT: B  601 MET cc_start: 0.7612 (mtt) cc_final: 0.7284 (mtt)
REVERT: B  684 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7676 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8023 (tppt)
  outliers start: 33
  outliers final: 25
  residues processed: 155
  average time/residue: 0.0941
  time to fit residues: 21.3276
Evaluate side-chains
  148 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 155 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 136 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 111 optimal weight:    0.0370
   chunk 77 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 734 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.179971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.142543 restraints weight = 13547.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141348 restraints weight = 18480.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.142656 restraints weight = 16531.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142496 restraints weight = 13115.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.142748 restraints weight = 11914.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12750  Z= 0.123
  Angle     :  0.537   7.024  17312  Z= 0.259
  Chirality :  0.037   0.312   2024
  Planarity :  0.004   0.041   2170
  Dihedral  :  5.343  45.628   1866
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.88 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.22), residues: 1592
  helix:  2.50 (0.16), residues: 1052
  sheet:  0.68 (0.39), residues: 162
  loop : -0.59 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 464 
 TYR   0.010   0.001   TYR A  93 
 PHE   0.026   0.001   PHE A 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.003   0.000   HIS B 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.12 (12750)
  covalent geometry    : angle       0.53730 /  0.26 (17312)
  hydrogen bonds       : bond        0.03446 /  2.34 (  849)
  hydrogen bonds       : angle       3.80240 /  2.74 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 VAL cc_start: 0.8175 (t) cc_final: 0.7901 (p)
REVERT: A  464 ARG cc_start: 0.7921 (mmt180) cc_final: 0.7492 (mmm160)
REVERT: A  601 MET cc_start: 0.7626 (mtt) cc_final: 0.7300 (mtt)
REVERT: A  684 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7681 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8026 (tppt)
REVERT: B  408 VAL cc_start: 0.8191 (t) cc_final: 0.7916 (p)
REVERT: B  464 ARG cc_start: 0.7919 (mmt180) cc_final: 0.7494 (mmm160)
REVERT: B  601 MET cc_start: 0.7616 (mtt) cc_final: 0.7293 (mtt)
REVERT: B  684 ARG cc_start: 0.8122 (ttp-110) cc_final: 0.7684 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8027 (tppt)
  outliers start: 31
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0963
  time to fit residues: 21.1241
Evaluate side-chains
  151 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 145 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.8384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.176517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139268 restraints weight = 13654.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.137630 restraints weight = 19558.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139337 restraints weight = 17574.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.138477 restraints weight = 13436.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.139200 restraints weight = 13633.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  12750  Z= 0.142
  Angle     :  0.560   7.667  17312  Z= 0.271
  Chirality :  0.038   0.316   2024
  Planarity :  0.004   0.040   2170
  Dihedral  :  5.521  48.302   1866
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.60 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.22), residues: 1592
  helix:  2.35 (0.16), residues: 1062
  sheet:  0.67 (0.40), residues: 162
  loop : -0.71 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.014   0.002   TYR A 136 
 PHE   0.026   0.001   PHE A 839 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.002   0.001   HIS B 788 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.14 (12750)
  covalent geometry    : angle       0.56029 /  0.27 (17312)
  hydrogen bonds       : bond        0.03695 /  2.50 (  849)
  hydrogen bonds       : angle       3.88619 /  2.79 ( 2487)

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

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

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3184 Ramachandran restraints generated.
    1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7525 (mmm160)
REVERT: A  601 MET cc_start: 0.7659 (mtt) cc_final: 0.7324 (mtt)
REVERT: A  684 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7691 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8024 (tppt)
REVERT: B  464 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7505 (mmm160)
REVERT: B  601 MET cc_start: 0.7663 (mtt) cc_final: 0.7340 (mtt)
REVERT: B  684 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7696 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8026 (tppt)
  outliers start: 28
  outliers final: 24
  residues processed: 141
  average time/residue: 0.1020
  time to fit residues: 20.9411
Evaluate side-chains
  147 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 MET
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 THR
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  765 ASP
Chi-restraints excluded: chain A residue  862 VAL
Chi-restraints excluded: chain B residue  107 MET
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  515 LEU
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  748 VAL
Chi-restraints excluded: chain B residue  765 ASP
Chi-restraints excluded: chain B residue  862 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 136 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 95 optimal weight:    7.9990
   chunk 118 optimal weight:    0.1980
   chunk 94 optimal weight:    6.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    1.2184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.178269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.141534 restraints weight = 13742.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.139424 restraints weight = 21461.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141253 restraints weight = 18741.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141439 restraints weight = 14394.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.141679 restraints weight = 14959.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12750  Z= 0.179
  Angle     :  0.600   7.977  17312  Z= 0.290
  Chirality :  0.039   0.319   2024
  Planarity :  0.005   0.039   2170
  Dihedral  :  5.918  54.327   1866
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.60 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.21), residues: 1592
  helix:  2.13 (0.16), residues: 1064
  sheet:  0.63 (0.40), residues: 162
  loop : -0.78 (0.35), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 464 
 TYR   0.014   0.002   TYR A  93 
 PHE   0.026   0.002   PHE A 839 
 TRP   0.009   0.001   TRP B 682 
 HIS   0.003   0.001   HIS B 566 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.18 (12750)
  covalent geometry    : angle       0.60044 /  0.29 (17312)
  hydrogen bonds       : bond        0.04109 /  2.79 (  849)
  hydrogen bonds       : angle       3.99333 /  2.88 ( 2487)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1706.54 seconds
wall clock time: 30 minutes 19.12 seconds (1819.12 seconds total)