Starting phenix.real_space_refine
on Wed Feb  4 20:17:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j8s_61240/02_2026/9j8s_61240.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j8s_61240/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j8s_61240/02_2026/9j8s_61240.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j8s_61240/02_2026/9j8s_61240.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j8s_61240/02_2026/9j8s_61240.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j8s_61240/02_2026/9j8s_61240.cif"
  }
  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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 74
          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: 4.87, per 1000 atoms: 0.39
  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: 0.80
  Conformation dependent library (CDL) restraints added in 513.9 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: 0.41
  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: 1.96

  Time building geometry restraints manager: 1.08 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 -    30.81: 7414
       30.81 -    61.61: 192
       61.61 -    92.42: 22
       92.42 -   123.22: 0
      123.22 -   154.03: 2
  Dihedral angle restraints: 7630
    sinusoidal: 3018
      harmonic: 4612
  Sorted by residual:
  dihedral pdb=" C3  PGT B 903 "
           pdb=" C1  PGT B 903 "
           pdb=" C2  PGT B 903 "
           pdb=" O3P PGT B 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.87  139.84  154.03     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" C3  PGT A 903 "
           pdb=" C1  PGT A 903 "
           pdb=" C2  PGT A 903 "
           pdb=" O3P PGT A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.87  139.84  154.03     1      3.00e+01 1.11e-03 2.03e+01
  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
  ... (remaining 7627 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:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.650
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6567
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  : 14.335 154.030   4654
  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
  covalent geometry    : bond        0.00704 (12750)
  covalent geometry    : angle       1.03341 (17312)
  hydrogen bonds       : bond        0.15556 (  849)
  hydrogen bonds       : angle       6.65771 ( 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  : 0.443 
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: 0.1430
  time to fit residues: 32.4566
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  : 0.443 
-------------------------------------------------------------------------------
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...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.177604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139658 restraints weight = 13610.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.139039 restraints weight = 19803.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140661 restraints weight = 16615.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140136 restraints weight = 13799.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.140483 restraints weight = 14051.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.1073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  12750  Z= 0.152
  Angle     :  0.572   7.675  17312  Z= 0.279
  Chirality :  0.037   0.199   2024
  Planarity :  0.004   0.034   2170
  Dihedral  :  8.400 151.597   1896
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  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:  1.63 (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   0.014   0.002   TYR A 680 
 PHE   0.012   0.001   PHE B  87 
 TRP   0.009   0.001   TRP B 446 
 HIS   0.003   0.001   HIS B 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (12750)
  covalent geometry    : angle       0.57188 (17312)
  hydrogen bonds       : bond        0.04318 (  849)
  hydrogen bonds       : angle       4.20834 ( 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  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7579 (mtt) cc_final: 0.7301 (mtt)
REVERT: B  601 MET cc_start: 0.7573 (mtt) cc_final: 0.7294 (mtt)
  outliers start: 26
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1208
  time to fit residues: 26.3957
Evaluate side-chains
  135 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0370
   chunk 67 optimal weight:    7.9990
   chunk 55 optimal weight:    0.4980
   chunk 106 optimal weight:    0.5980
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B 400 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.176882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.139314 restraints weight = 13607.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.138088 restraints weight = 20243.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.140101 restraints weight = 17177.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.138988 restraints weight = 14372.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.139572 restraints weight = 12582.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12750  Z= 0.117
  Angle     :  0.520   5.924  17312  Z= 0.252
  Chirality :  0.035   0.226   2024
  Planarity :  0.004   0.038   2170
  Dihedral  :  8.179 149.367   1896
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 10.24 %
    Favored  : 86.72 %
  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:  2.16 (0.21), residues: 1592
  helix:  2.36 (0.15), residues: 1052
  sheet:  0.34 (0.38), residues: 162
  loop : -0.78 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 684 
 TYR   0.018   0.001   TYR A 680 
 PHE   0.013   0.001   PHE A 780 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.004   0.000   HIS B 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12750)
  covalent geometry    : angle       0.52016 (17312)
  hydrogen bonds       : bond        0.03751 (  849)
  hydrogen bonds       : angle       3.91952 ( 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
  174 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  684 ARG cc_start: 0.7994 (ttp-110) cc_final: 0.7624 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8095 (tppt)
REVERT: B  601 MET cc_start: 0.7614 (mtt) cc_final: 0.7369 (mtt)
REVERT: B  684 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7621 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8468 (mtmt) cc_final: 0.8095 (tppt)
  outliers start: 38
  outliers final: 20
  residues processed: 158
  average time/residue: 0.1070
  time to fit residues: 23.9662
Evaluate side-chains
  142 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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  298 LEU
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  746 LYS
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  298 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  746 LYS
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:    0.9980
   chunk 133 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 144 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 90 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 140 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.178320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.139671 restraints weight = 13570.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.137885 restraints weight = 21982.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.140120 restraints weight = 17827.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.139270 restraints weight = 13633.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139677 restraints weight = 12490.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12750  Z= 0.141
  Angle     :  0.526   5.528  17312  Z= 0.254
  Chirality :  0.036   0.225   2024
  Planarity :  0.004   0.039   2170
  Dihedral  :  8.252 148.733   1896
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 10.56 %
    Favored  : 85.76 %
  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:  2.22 (0.21), residues: 1592
  helix:  2.40 (0.15), residues: 1050
  sheet:  0.49 (0.39), residues: 162
  loop : -0.78 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 660 
 TYR   0.016   0.002   TYR B 680 
 PHE   0.023   0.001   PHE B 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.004   0.001   HIS A 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12750)
  covalent geometry    : angle       0.52560 (17312)
  hydrogen bonds       : bond        0.03821 (  849)
  hydrogen bonds       : angle       3.91560 ( 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
  170 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 124
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7516 (mtt) cc_final: 0.7261 (mtt)
REVERT: B  601 MET cc_start: 0.7677 (mtt) cc_final: 0.7384 (mtt)
  outliers start: 46
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1107
  time to fit residues: 25.1270
Evaluate side-chains
  143 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  298 LEU
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  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  298 LEU
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 58 optimal weight:    0.3980
   chunk 94 optimal weight:    3.9990
   chunk 159 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 153 optimal weight:    0.6980
   chunk 67 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.178542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140290 restraints weight = 13668.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.138768 restraints weight = 21760.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140577 restraints weight = 18373.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.140277 restraints weight = 14380.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.140489 restraints weight = 12906.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12750  Z= 0.129
  Angle     :  0.518   5.456  17312  Z= 0.251
  Chirality :  0.036   0.255   2024
  Planarity :  0.004   0.039   2170
  Dihedral  :  8.184 147.544   1896
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 11.20 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.46 (0.15), residues: 1048
  sheet:  0.55 (0.39), residues: 162
  loop : -0.74 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 684 
 TYR   0.016   0.002   TYR A 680 
 PHE   0.023   0.001   PHE B 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.003   0.000   HIS B 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12750)
  covalent geometry    : angle       0.51835 (17312)
  hydrogen bonds       : bond        0.03649 (  849)
  hydrogen bonds       : angle       3.86014 ( 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
  170 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 124
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7605 (mtt) cc_final: 0.7308 (mtt)
REVERT: A  602 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8201 (mm)
REVERT: B  601 MET cc_start: 0.7650 (mtt) cc_final: 0.7334 (mtt)
  outliers start: 46
  outliers final: 26
  residues processed: 160
  average time/residue: 0.1014
  time to fit residues: 23.4975
Evaluate side-chains
  149 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  298 LEU
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  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  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  298 LEU
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  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:    0.9990
   chunk 32 optimal weight:    0.0770
   chunk 122 optimal weight:    0.9990
   chunk 77 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0980
   chunk 38 optimal weight:    0.4980
   chunk 132 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 148 optimal weight:    0.2980
   chunk 153 optimal weight:    9.9990
   chunk 112 optimal weight:    0.4980
   overall best weight:    0.2938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.181641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140056 restraints weight = 13609.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.139382 restraints weight = 15360.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.141503 restraints weight = 13188.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141438 restraints weight = 10260.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141331 restraints weight = 9874.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12750  Z= 0.102
  Angle     :  0.510   6.328  17312  Z= 0.244
  Chirality :  0.035   0.277   2024
  Planarity :  0.004   0.039   2170
  Dihedral  :  7.976 144.731   1896
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 11.76 %
    Favored  : 84.88 %
  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:  2.49 (0.21), residues: 1592
  helix:  2.58 (0.16), residues: 1052
  sheet:  0.57 (0.39), residues: 162
  loop : -0.59 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 524 
 TYR   0.016   0.001   TYR A 680 
 PHE   0.024   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
  covalent geometry    : bond        0.00229 (12750)
  covalent geometry    : angle       0.50952 (17312)
  hydrogen bonds       : bond        0.03263 (  849)
  hydrogen bonds       : angle       3.75069 ( 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
  180 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7610 (mtt) cc_final: 0.7237 (mtt)
REVERT: A  602 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8094 (mm)
REVERT: A  706 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8018 (tppt)
REVERT: B  601 MET cc_start: 0.7659 (mtt) cc_final: 0.7350 (mtt)
REVERT: B  602 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7915 (mm)
REVERT: B  706 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8022 (tppt)
  outliers start: 42
  outliers final: 26
  residues processed: 166
  average time/residue: 0.1027
  time to fit residues: 24.7493
Evaluate side-chains
  149 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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  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  746 LYS
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  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  602 ILE
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  746 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 111 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 116 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 99 optimal weight:   10.0000
   chunk 113 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 105 optimal weight:    0.0970
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.3754

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

Flipped N/Q/H residues before XYZ refinement:
A 734 ASN
B 734 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.182302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.145067 restraints weight = 13472.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.142095 restraints weight = 19729.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143150 restraints weight = 17160.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.142888 restraints weight = 14040.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.143206 restraints weight = 11985.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.066  12750  Z= 0.107
  Angle     :  0.516   8.139  17312  Z= 0.247
  Chirality :  0.035   0.275   2024
  Planarity :  0.004   0.041   2170
  Dihedral  :  7.847 142.141   1896
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.92 %
    Favored  : 85.04 %
  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:  2.56 (0.21), residues: 1592
  helix:  2.66 (0.16), residues: 1052
  sheet:  0.50 (0.38), residues: 162
  loop : -0.62 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 524 
 TYR   0.016   0.001   TYR A 136 
 PHE   0.025   0.001   PHE B 839 
 TRP   0.009   0.001   TRP B 446 
 HIS   0.003   0.000   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (12750)
  covalent geometry    : angle       0.51610 (17312)
  hydrogen bonds       : bond        0.03193 (  849)
  hydrogen bonds       : angle       3.71123 ( 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
  170 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7626 (mtt) cc_final: 0.7308 (mtt)
REVERT: A  684 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7611 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8553 (mtmm) cc_final: 0.7985 (tppt)
REVERT: B  601 MET cc_start: 0.7653 (mtt) cc_final: 0.7339 (mtt)
REVERT: B  602 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.7939 (mm)
REVERT: B  684 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7611 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7989 (tppt)
  outliers start: 38
  outliers final: 30
  residues processed: 158
  average time/residue: 0.0969
  time to fit residues: 22.8452
Evaluate side-chains
  155 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 124
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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  746 LYS
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  602 ILE
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  651 THR
Chi-restraints excluded: chain B residue  746 LYS
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:    0.6980
   chunk 159 optimal weight:    5.9990
   chunk 149 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0050
   chunk 147 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0020
   chunk 155 optimal weight:    0.6980
   overall best weight:    0.4602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.177969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.139714 restraints weight = 13358.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.138680 restraints weight = 18670.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140516 restraints weight = 16496.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.140273 restraints weight = 12580.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.140987 restraints weight = 11736.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12750  Z= 0.110
  Angle     :  0.517   7.362  17312  Z= 0.247
  Chirality :  0.036   0.310   2024
  Planarity :  0.004   0.041   2170
  Dihedral  :  7.810 140.576   1896
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 12.88 %
    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:  2.55 (0.21), residues: 1592
  helix:  2.65 (0.16), residues: 1052
  sheet:  0.51 (0.38), residues: 162
  loop : -0.62 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 524 
 TYR   0.013   0.001   TYR B 680 
 PHE   0.025   0.001   PHE B 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.002   0.000   HIS B 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12750)
  covalent geometry    : angle       0.51734 (17312)
  hydrogen bonds       : bond        0.03235 (  849)
  hydrogen bonds       : angle       3.74248 ( 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
  167 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 130
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7691 (mtt) cc_final: 0.7403 (mtt)
REVERT: A  684 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7596 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8067 (tppt)
REVERT: B  601 MET cc_start: 0.7664 (mtt) cc_final: 0.7346 (mtt)
REVERT: B  602 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7950 (mm)
REVERT: B  684 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7600 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8070 (tppt)
  outliers start: 37
  outliers final: 29
  residues processed: 154
  average time/residue: 0.1029
  time to fit residues: 23.5515
Evaluate side-chains
  160 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
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  249 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  276 LEU
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  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  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  276 LEU
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  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  792 GLN
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:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 155 optimal weight:    0.0060
   chunk 1 optimal weight:    0.6980
   chunk 136 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.181190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144168 restraints weight = 13523.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.142464 restraints weight = 18134.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.143376 restraints weight = 16689.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.141015 restraints weight = 16833.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.142703 restraints weight = 14234.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  12750  Z= 0.117
  Angle     :  0.534   7.113  17312  Z= 0.257
  Chirality :  0.037   0.302   2024
  Planarity :  0.004   0.041   2170
  Dihedral  :  7.805 139.184   1896
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.52 %
    Favored  : 83.68 %
  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:  2.46 (0.22), residues: 1592
  helix:  2.56 (0.16), residues: 1052
  sheet:  0.60 (0.39), residues: 162
  loop : -0.64 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 524 
 TYR   0.016   0.001   TYR B 136 
 PHE   0.026   0.001   PHE B 839 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.002   0.000   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12750)
  covalent geometry    : angle       0.53394 (17312)
  hydrogen bonds       : bond        0.03360 (  849)
  hydrogen bonds       : angle       3.75833 ( 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
  165 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7601 (mtt) cc_final: 0.7311 (mtt)
REVERT: A  684 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7649 (ttm-80)
REVERT: A  706 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8047 (tppt)
REVERT: B  601 MET cc_start: 0.7581 (mtt) cc_final: 0.7243 (mtt)
REVERT: B  602 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.7966 (mm)
REVERT: B  684 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7651 (ttm-80)
REVERT: B  706 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8043 (tppt)
  outliers start: 35
  outliers final: 31
  residues processed: 153
  average time/residue: 0.1023
  time to fit residues: 23.2511
Evaluate side-chains
  153 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
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  249 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  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  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  430 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  515 LEU
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  792 GLN
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:    3.9990
   chunk 136 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 145 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   chunk 74 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0570
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5698

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.177254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.140866 restraints weight = 13517.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.139520 restraints weight = 18770.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140986 restraints weight = 17304.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.140092 restraints weight = 13615.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140396 restraints weight = 13250.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  12750  Z= 0.118
  Angle     :  0.532   6.889  17312  Z= 0.256
  Chirality :  0.037   0.330   2024
  Planarity :  0.004   0.041   2170
  Dihedral  :  7.783 137.833   1896
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 13.44 %
    Favored  : 83.76 %
  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:  2.44 (0.22), residues: 1592
  helix:  2.55 (0.16), residues: 1054
  sheet:  0.61 (0.39), residues: 162
  loop : -0.69 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 419 
 TYR   0.011   0.001   TYR B 680 
 PHE   0.026   0.001   PHE B 839 
 TRP   0.009   0.001   TRP A 446 
 HIS   0.003   0.000   HIS B 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (12750)
  covalent geometry    : angle       0.53239 (17312)
  hydrogen bonds       : bond        0.03347 (  849)
  hydrogen bonds       : angle       3.76653 ( 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
  162 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 MET cc_start: 0.7614 (mtt) cc_final: 0.7307 (mtt)
REVERT: A  706 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8025 (tppt)
REVERT: B   85 LEU cc_start: 0.7972 (tp) cc_final: 0.7666 (tt)
REVERT: B  601 MET cc_start: 0.7608 (mtt) cc_final: 0.7284 (mtt)
REVERT: B  602 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: B  706 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8026 (tppt)
  outliers start: 35
  outliers final: 30
  residues processed: 151
  average time/residue: 0.1025
  time to fit residues: 22.8291
Evaluate side-chains
  157 residues out of total 1250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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  430 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  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  430 VAL
Chi-restraints excluded: chain B residue  496 LEU
Chi-restraints excluded: chain B residue  515 LEU
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  792 GLN
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:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 136 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0670
   chunk 118 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.7922

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.178805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141262 restraints weight = 13635.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140007 restraints weight = 19338.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.140953 restraints weight = 16761.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140893 restraints weight = 14813.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.141308 restraints weight = 12644.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  12750  Z= 0.137
  Angle     :  0.557   7.729  17312  Z= 0.268
  Chirality :  0.037   0.332   2024
  Planarity :  0.004   0.040   2170
  Dihedral  :  7.904 138.087   1896
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 13.36 %
    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:  2.31 (0.22), residues: 1592
  helix:  2.42 (0.16), residues: 1054
  sheet:  0.65 (0.39), residues: 162
  loop : -0.69 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 684 
 TYR   0.012   0.001   TYR B  93 
 PHE   0.026   0.001   PHE B 839 
 TRP   0.008   0.001   TRP A 446 
 HIS   0.002   0.000   HIS B 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12750)
  covalent geometry    : angle       0.55688 (17312)
  hydrogen bonds       : bond        0.03586 (  849)
  hydrogen bonds       : angle       3.83976 ( 2487)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1690.92 seconds
wall clock time: 29 minutes 56.57 seconds (1796.57 seconds total)