Starting phenix.real_space_refine
on Fri Jul  3 05:16:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i96_35258/07_2026/8i96_35258.map"
  }
  resolution = 3.2
  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=  -0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    7950      2.51       5
     N    2110      2.21       5
     O    2284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12404
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 6170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 763, 6170
          Classifications: {'peptide': 763}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 33, 'TRANS': 727}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GJX': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    A
  Time building chain proxies: 5.85, per 1000 atoms: 0.47
  Number of scatterers: 12404
  At special positions: 0
  Unit cell: (103.418, 126.658, 105.742, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    2284      8.00
     N    2110      7.00
     C    7950      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  36 " - pdb=" SG  CYS B  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  98 " - pdb=" SG  CYS B 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 100 " - pdb=" SG  CYS B 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 183 " - pdb=" SG  CYS B 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 263 " - pdb=" SG  CYS B 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 491 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 787 " - pdb=" SG  CYS B 814 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 789 " - pdb=" SG  CYS B 833 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  36 " - pdb=" SG  CYS A  51 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 475 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 112 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 263 " - pdb=" SG  CYS A 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 491 " - pdb=" SG  CYS A 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 787 " - pdb=" SG  CYS A 814 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 789 " - pdb=" SG  CYS A 833 " distance=2.03

  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: 0.98
  Conformation dependent library (CDL) restraints added in 560.1 milliseconds
  

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2960

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 12 sheets defined
      14.9% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.761A  pdb=" N   ALA B 172 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 277
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 326 through 333
      removed outlier: 3.844A  pdb=" N   GLY B 331 " --> pdb=" O   ALA B 327 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP B 332 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.602A  pdb=" N   LEU B 339 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 369
    Processing helix  chain 'B' and resid 387 through 396
      removed outlier: 3.514A  pdb=" N   SER B 391 " --> pdb=" O   PHE B 388 " (cutoff:3.500A)
      Proline residue:  B 392  - end of helix
      removed outlier: 4.252A  pdb=" N   ASN B 395 " --> pdb=" O   PRO B 392 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B 396 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 419
      removed outlier: 3.797A  pdb=" N   GLN B 419 " --> pdb=" O   MET B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 581
      removed outlier: 4.049A  pdb=" N   PHE B 580 " --> pdb=" O   ASN B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 635
      removed outlier: 3.882A  pdb=" N   LEU B 634 " --> pdb=" O   HIS B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 641 through 645
      removed outlier: 4.425A  pdb=" N   GLN B 644 " --> pdb=" O   ARG B 641 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 645 " --> pdb=" O   TYR B 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 641 through 645'
    Processing helix  chain 'B' and resid 668 through 673
    Processing helix  chain 'B' and resid 692 through 698
      removed outlier: 3.573A  pdb=" N   ARG B 696 " --> pdb=" O   GLU B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 722
    Processing helix  chain 'B' and resid 768 through 773
    Processing helix  chain 'B' and resid 788 through 790
      No H-bonds generated for 'chain 'B' and resid 788 through 790'
    Processing helix  chain 'B' and resid 791 through 799
    Processing helix  chain 'B' and resid 817 through 819
      No H-bonds generated for 'chain 'B' and resid 817 through 819'
    Processing helix  chain 'B' and resid 826 through 828
      No H-bonds generated for 'chain 'B' and resid 826 through 828'
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 3.761A  pdb=" N   ALA A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 277
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'A' and resid 326 through 333
      removed outlier: 3.843A  pdb=" N   GLY A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.601A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 369
    Processing helix  chain 'A' and resid 387 through 396
      removed outlier: 3.514A  pdb=" N   SER A 391 " --> pdb=" O   PHE A 388 " (cutoff:3.500A)
      Proline residue:  A 392  - end of helix
      removed outlier: 4.252A  pdb=" N   ASN A 395 " --> pdb=" O   PRO A 392 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A 396 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 419
      removed outlier: 3.797A  pdb=" N   GLN A 419 " --> pdb=" O   MET A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 581
      removed outlier: 4.050A  pdb=" N   PHE A 580 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 3.882A  pdb=" N   LEU A 634 " --> pdb=" O   HIS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 645
      removed outlier: 4.426A  pdb=" N   GLN A 644 " --> pdb=" O   ARG A 641 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 645 " --> pdb=" O   TYR A 642 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 641 through 645'
    Processing helix  chain 'A' and resid 668 through 673
    Processing helix  chain 'A' and resid 692 through 698
      removed outlier: 3.573A  pdb=" N   ARG A 696 " --> pdb=" O   GLU A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 722
    Processing helix  chain 'A' and resid 768 through 773
    Processing helix  chain 'A' and resid 788 through 790
      No H-bonds generated for 'chain 'A' and resid 788 through 790'
    Processing helix  chain 'A' and resid 791 through 799
    Processing helix  chain 'A' and resid 817 through 819
      No H-bonds generated for 'chain 'A' and resid 817 through 819'
    Processing helix  chain 'A' and resid 826 through 828
      No H-bonds generated for 'chain 'A' and resid 826 through 828'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 41
      removed outlier: 6.896A  pdb=" N   LEU B  70 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ILE B  94 " --> pdb=" O   TYR B 133 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LEU B 132 " --> pdb=" O   SER B 154 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LEU B 209 " --> pdb=" O   TYR B 231 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU B 319 " --> pdb=" O   ASP B 346 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU B 345 " --> pdb=" O   ARG B 376 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 375 " --> pdb=" O   ASP B 403 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   LEU B 402 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   LEU B 498 " --> pdb=" O   ASN B 523 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU B 522 " --> pdb=" O   ASP B 548 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU B 547 " --> pdb=" O   ASP B 572 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU B 571 " --> pdb=" O   MET B 602 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LEU B 601 " --> pdb=" O   GLU B 625 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU B 680 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 80
    Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 163
    Processing sheet with id=AA4, first strand: chain 'B' and resid 530 through 531
      removed outlier: 3.635A  pdb=" N   GLN B 531 " --> pdb=" O   ARG B 553 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 727 through 729
      removed outlier: 7.393A  pdb=" N   LEU B 752 " --> pdb=" O   LEU B 779 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 813 through 815
      removed outlier: 4.929A  pdb=" N   CYS B 814 " --> pdb=" O   GLY B 822 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 37 through 41
      removed outlier: 6.897A  pdb=" N   LEU A  70 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   ILE A  94 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   LEU A 132 " --> pdb=" O   SER A 154 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A 209 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LEU A 319 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU A 345 " --> pdb=" O   ARG A 376 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LEU A 375 " --> pdb=" O   ASP A 403 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   LEU A 402 " --> pdb=" O   ASP A 427 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   LEU A 498 " --> pdb=" O   ASN A 523 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LEU A 522 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU A 547 " --> pdb=" O   ASP A 572 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU A 571 " --> pdb=" O   MET A 602 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LEU A 601 " --> pdb=" O   GLU A 625 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU A 680 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 79 through 80
    Processing sheet with id=AA9, first strand: chain 'A' and resid 162 through 163
    Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 531
      removed outlier: 3.635A  pdb=" N   GLN A 531 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 727 through 729
      removed outlier: 7.393A  pdb=" N   LEU A 752 " --> pdb=" O   LEU A 779 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 813 through 815
      removed outlier: 4.929A  pdb=" N   CYS A 814 " --> pdb=" O   GLY A 822 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    234 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3986
        1.34 -     1.46: 1645
        1.46 -     1.57: 6957
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 12670
  Sorted by residual:
  bond pdb=" N1  GJX B 901 "
       pdb=" O3  GJX B 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.391 -0.185 2.00e-02 2.50e+03 8.57e+01
  bond pdb=" N1  GJX A 901 "
       pdb=" O3  GJX A 901 "
    ideal  model  delta    sigma   weight residual
    1.206  1.391 -0.185 2.00e-02 2.50e+03 8.55e+01
  bond pdb=" N1  GJX B 901 "
       pdb=" O2  GJX B 901 "
    ideal  model  delta    sigma   weight residual
    1.211  1.391 -0.180 2.00e-02 2.50e+03 8.11e+01
  bond pdb=" N1  GJX A 901 "
       pdb=" O2  GJX A 901 "
    ideal  model  delta    sigma   weight residual
    1.211  1.391 -0.180 2.00e-02 2.50e+03 8.06e+01
  bond pdb=" C2  GJX B 901 "
       pdb=" C7  GJX B 901 "
    ideal  model  delta    sigma   weight residual
    1.418  1.486 -0.068 2.00e-02 2.50e+03 1.16e+01
  ... (remaining 12665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.62: 17145
        5.62 -    11.25: 23
       11.25 -    16.87: 12
       16.87 -    22.50: 0
       22.50 -    28.12: 2
  Bond angle restraints: 17182
  Sorted by residual:
  angle pdb=" C18 GJX A 901 "
        pdb=" C20 GJX A 901 "
        pdb=" C21 GJX A 901 "
      ideal   model   delta    sigma   weight residual
     112.69   84.57   28.12 3.00e+00 1.11e-01 8.79e+01
  angle pdb=" C18 GJX B 901 "
        pdb=" C20 GJX B 901 "
        pdb=" C21 GJX B 901 "
      ideal   model   delta    sigma   weight residual
     112.69   84.58   28.11 3.00e+00 1.11e-01 8.78e+01
  angle pdb=" C14 GJX A 901 "
        pdb=" C23 GJX A 901 "
        pdb=" C21 GJX A 901 "
      ideal   model   delta    sigma   weight residual
     110.36   95.29   15.07 3.00e+00 1.11e-01 2.52e+01
  angle pdb=" C14 GJX B 901 "
        pdb=" C23 GJX B 901 "
        pdb=" C21 GJX B 901 "
      ideal   model   delta    sigma   weight residual
     110.36   95.30   15.06 3.00e+00 1.11e-01 2.52e+01
  angle pdb=" C14 GJX A 901 "
        pdb=" C15 GJX A 901 "
        pdb=" C18 GJX A 901 "
      ideal   model   delta    sigma   weight residual
     110.49   95.53   14.96 3.00e+00 1.11e-01 2.49e+01
  ... (remaining 17177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 6954
       17.41 -    34.83: 661
       34.83 -    52.24: 159
       52.24 -    69.66: 50
       69.66 -    87.07: 14
  Dihedral angle restraints: 7838
    sinusoidal: 3310
      harmonic: 4528
  Sorted by residual:
  dihedral pdb=" CB  CYS A 263 "
           pdb=" SG  CYS A 263 "
           pdb=" SG  CYS A 270 "
           pdb=" CB  CYS A 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.03  -72.03     1      1.00e+01 1.00e-02 6.64e+01
  dihedral pdb=" CB  CYS B 263 "
           pdb=" SG  CYS B 263 "
           pdb=" SG  CYS B 270 "
           pdb=" CB  CYS B 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.02  -72.02     1      1.00e+01 1.00e-02 6.64e+01
  dihedral pdb=" CB  CYS B 789 "
           pdb=" SG  CYS B 789 "
           pdb=" SG  CYS B 833 "
           pdb=" CB  CYS B 833 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.29  -67.29     1      1.00e+01 1.00e-02 5.89e+01
  ... (remaining 7835 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.397: 1970
       0.397 -    0.795: 0
       0.795 -    1.192: 0
       1.192 -    1.589: 0
       1.589 -    1.987: 4
  Chirality restraints: 1974
  Sorted by residual:
  chirality pdb=" C21 GJX A 901 "
            pdb=" C19 GJX A 901 "
            pdb=" C20 GJX A 901 "
            pdb=" C23 GJX A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -0.81   -1.99 2.00e-01 2.50e+01 9.87e+01
  chirality pdb=" C21 GJX B 901 "
            pdb=" C19 GJX B 901 "
            pdb=" C20 GJX B 901 "
            pdb=" C23 GJX B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.80   -0.81   -1.99 2.00e-01 2.50e+01 9.86e+01
  chirality pdb=" C18 GJX A 901 "
            pdb=" C15 GJX A 901 "
            pdb=" C20 GJX A 901 "
            pdb=" C22 GJX A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -0.81   -1.99 2.00e-01 2.50e+01 9.85e+01
  ... (remaining 1971 not shown)

  Planarity restraints: 2182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" O   GJX B 901 "   -0.515 2.00e-02 2.50e+03   3.88e-01 2.26e+03
        pdb=" C11 GJX B 901 "    0.486 2.00e-02 2.50e+03
        pdb=" C12 GJX B 901 "   -0.417 2.00e-02 2.50e+03
        pdb=" C13 GJX B 901 "   -0.042 2.00e-02 2.50e+03
        pdb=" C14 GJX B 901 "    0.477 2.00e-02 2.50e+03
        pdb=" N3  GJX B 901 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" O   GJX A 901 "    0.515 2.00e-02 2.50e+03   3.88e-01 2.26e+03
        pdb=" C11 GJX A 901 "   -0.486 2.00e-02 2.50e+03
        pdb=" C12 GJX A 901 "    0.417 2.00e-02 2.50e+03
        pdb=" C13 GJX A 901 "    0.042 2.00e-02 2.50e+03
        pdb=" C14 GJX A 901 "   -0.476 2.00e-02 2.50e+03
        pdb=" N3  GJX A 901 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 101 "    0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A 102 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "    0.028 5.00e-02 4.00e+02
  ... (remaining 2179 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 386
        2.71 -     3.26: 12014
        3.26 -     3.81: 19448
        3.81 -     4.35: 26805
        4.35 -     4.90: 43891
  Nonbonded interactions: 102544
  Sorted by model distance:
  nonbonded pdb=" O   THR B 832 "
            pdb=" OG1 THR B 832 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   THR A 832 "
            pdb=" OG1 THR A 832 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" O   LEU A 179 "
            pdb=" ND2 ASN A 214 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   LEU B 179 "
            pdb=" ND2 ASN B 214 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   SER B 504 "
            pdb=" OG  SER B 504 "
     model   vdw
     2.302 3.040
  ... (remaining 102539 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 'B'
  selection = chain 'A'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.420
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.185  12686  Z= 0.227
  Angle     :  0.777  28.122  17214  Z= 0.345
  Chirality :  0.099   1.987   1974
  Planarity :  0.012   0.388   2182
  Dihedral  : 14.997  87.072   4830
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.10 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 10.17 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    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: -3.43 (0.19), residues: 1514
  helix: -4.70 (0.23), residues: 100
  sheet: -2.77 (0.31), residues: 278
  loop : -2.04 (0.16), residues: 1136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 121 
 TYR   0.013   0.001   TYR A 751 
 PHE   0.007   0.001   PHE A 506 
 TRP   0.003   0.000   TRP A 797 
 HIS   0.004   0.001   HIS B  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00444 /  0.23 (12670)
  covalent geometry    : angle       0.77744 /  0.34 (17182)
  SS BOND              : bond        0.00100 /  0.07 (   16)
  SS BOND              : angle       0.32599 /  0.19 (   32)
  hydrogen bonds       : bond        0.28214 / 18.60 (  128)
  hydrogen bonds       : angle       7.92566 /  5.36 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 196
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.6858 (t80) cc_final: 0.6523 (t80)
REVERT: B  197 LYS cc_start: 0.8259 (tptt) cc_final: 0.7657 (tttt)
REVERT: B  501 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7823 (p)
REVERT: B  534 ASN cc_start: 0.7204 (p0) cc_final: 0.6901 (p0)
REVERT: B  616 MET cc_start: 0.7302 (mtp) cc_final: 0.7023 (mtp)
REVERT: B  734 GLN cc_start: 0.6507 (mp10) cc_final: 0.6049 (mp10)
REVERT: B  740 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.4528 (tptt)
REVERT: B  770 ASN cc_start: 0.7730 (t0) cc_final: 0.7525 (t0)
REVERT: B  828 LEU cc_start: 0.4267 (OUTLIER) cc_final: 0.3569 (tt)
REVERT: A  197 LYS cc_start: 0.7960 (tptt) cc_final: 0.7468 (tttt)
REVERT: A  353 LEU cc_start: 0.7783 (mt) cc_final: 0.7485 (mp)
REVERT: A  616 MET cc_start: 0.7430 (mtp) cc_final: 0.7080 (mtp)
REVERT: A  752 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7502 (tt)
  outliers start: 50
  outliers final: 29
  residues processed: 241
  average time/residue: 0.1125
  time to fit residues: 38.6934
Evaluate side-chains
  151 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  491 CYS
Chi-restraints excluded: chain B residue  501 SER
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  740 LYS
Chi-restraints excluded: chain B residue  756 SER
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  766 SER
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  826 ILE
Chi-restraints excluded: chain B residue  828 LEU
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain B residue  832 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  669 VAL
Chi-restraints excluded: chain A residue  740 LYS
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  783 ASN
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  832 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    2.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  75 ASN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
B 159 ASN
B 167 GLN
B 187 ASN
B 252 GLN
B 314 ASN
B 350 ASN
B 354 GLN
B 364 GLN
B 407 ASN
B 503 ASN
B 599 GLN
B 727 ASN
B 757 ASN
B 760 GLN
B 781 HIS
A  75 ASN
A  76 HIS
A  99 ASN
A 138 GLN
A 159 ASN
A 241 GLN
A 252 GLN
A 314 ASN
A 350 ASN
A 354 GLN
A 364 GLN
A 407 ASN
A 503 ASN
A 599 GLN
A 727 ASN
A 757 ASN
A 760 GLN

Total number of N/Q/H flips: 34

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.213916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.188973 restraints weight = 12006.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 1.06
r_work: 0.3782 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12686  Z= 0.204
  Angle     :  0.647   9.393  17214  Z= 0.322
  Chirality :  0.047   0.189   1974
  Planarity :  0.004   0.051   2182
  Dihedral  :  6.665  58.951   1785
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.81 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.65 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.75 (0.20), residues: 1514
  helix: -4.17 (0.27), residues: 102
  sheet: -2.91 (0.33), residues: 248
  loop : -1.43 (0.17), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 627 
 TYR   0.017   0.002   TYR A 233 
 PHE   0.027   0.002   PHE A  96 
 TRP   0.008   0.001   TRP B 793 
 HIS   0.004   0.001   HIS B 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.20 (12670)
  covalent geometry    : angle       0.64650 /  0.32 (17182)
  SS BOND              : bond        0.00782 /  0.31 (   16)
  SS BOND              : angle       0.89307 /  0.56 (   32)
  hydrogen bonds       : bond        0.04073 /  2.57 (  128)
  hydrogen bonds       : angle       5.49909 /  3.77 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 137
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.7531 (t80) cc_final: 0.7170 (t80)
REVERT: B  197 LYS cc_start: 0.8523 (tptt) cc_final: 0.8116 (ttpt)
REVERT: B  274 LYS cc_start: 0.7422 (ptmm) cc_final: 0.7172 (ptpt)
REVERT: B  602 MET cc_start: 0.8730 (mtm) cc_final: 0.8434 (mpp)
REVERT: A  197 LYS cc_start: 0.8288 (tptt) cc_final: 0.7864 (ttpt)
REVERT: A  588 MET cc_start: 0.8557 (mmm) cc_final: 0.8292 (mmm)
REVERT: A  616 MET cc_start: 0.7980 (mtp) cc_final: 0.7732 (mtp)
  outliers start: 50
  outliers final: 28
  residues processed: 182
  average time/residue: 0.0879
  time to fit residues: 25.0304
Evaluate side-chains
  144 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  491 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  756 SER
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain B residue  832 THR
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  122 SER
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  759 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  832 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 21 optimal weight:    0.0570
   chunk 56 optimal weight:    6.9990
   chunk 118 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 125 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 108 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0370
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
B 181 GLN
B 341 ASN
B 503 ASN
B 604 ASN
B 710 GLN
B 757 ASN
A 167 GLN
A 341 ASN
A 503 ASN
A 710 GLN
A 757 ASN
A 781 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.217887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.193115 restraints weight = 11961.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.4116 rms_B_bonded: 1.01
r_work: 0.3805 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12686  Z= 0.092
  Angle     :  0.500   7.368  17214  Z= 0.255
  Chirality :  0.043   0.173   1974
  Planarity :  0.003   0.051   2182
  Dihedral  :  5.524  57.533   1755
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.56 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.04 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.21), residues: 1514
  helix: -3.98 (0.30), residues: 102
  sheet: -2.76 (0.33), residues: 248
  loop : -1.18 (0.18), residues: 1164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 104 
 TYR   0.021   0.001   TYR A 233 
 PHE   0.014   0.001   PHE A 785 
 TRP   0.010   0.001   TRP A 793 
 HIS   0.002   0.000   HIS B 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00206 /  0.09 (12670)
  covalent geometry    : angle       0.49958 /  0.25 (17182)
  SS BOND              : bond        0.00157 /  0.12 (   16)
  SS BOND              : angle       0.55468 /  0.36 (   32)
  hydrogen bonds       : bond        0.03135 /  1.97 (  128)
  hydrogen bonds       : angle       5.27863 /  3.60 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.7457 (t80) cc_final: 0.7077 (t80)
REVERT: B  197 LYS cc_start: 0.8508 (tptt) cc_final: 0.8060 (ttpt)
REVERT: B  274 LYS cc_start: 0.7516 (ptmm) cc_final: 0.7296 (ptpt)
REVERT: B  602 MET cc_start: 0.8688 (mtm) cc_final: 0.8442 (mtm)
REVERT: A  197 LYS cc_start: 0.8319 (tptt) cc_final: 0.7867 (ttpt)
REVERT: A  236 MET cc_start: 0.8012 (ttm) cc_final: 0.7779 (tpp)
REVERT: A  588 MET cc_start: 0.8559 (mmm) cc_final: 0.8275 (mmm)
REVERT: A  616 MET cc_start: 0.7919 (mtp) cc_final: 0.7628 (mtp)
  outliers start: 35
  outliers final: 22
  residues processed: 159
  average time/residue: 0.0902
  time to fit residues: 22.2250
Evaluate side-chains
  135 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  431 ASN
Chi-restraints excluded: chain B residue  491 CYS
Chi-restraints excluded: chain B residue  699 LYS
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  431 ASN
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  757 ASN
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  832 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 135 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:   40.0000
   chunk 143 optimal weight:   10.0000
   chunk 147 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0570
   chunk 38 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 146 optimal weight:    9.9990
   overall best weight:    3.4106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  45 ASN
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 GLN
B 241 GLN
B 757 ASN
B 800 HIS
A  45 ASN
A 167 GLN
A 275 ASN
A 354 GLN
A 800 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.204615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.178529 restraints weight = 12011.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 1.06
r_work: 0.3702 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3636 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  12686  Z= 0.290
  Angle     :  0.688   9.383  17214  Z= 0.345
  Chirality :  0.050   0.201   1974
  Planarity :  0.005   0.050   2182
  Dihedral  :  5.446  57.784   1743
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  7.33 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.04 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.37 (0.21), residues: 1514
  helix: -3.79 (0.32), residues: 110
  sheet: -2.81 (0.33), residues: 248
  loop : -1.10 (0.18), residues: 1156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 378 
 TYR   0.018   0.002   TYR A 233 
 PHE   0.018   0.003   PHE B 646 
 TRP   0.009   0.001   TRP B 692 
 HIS   0.006   0.001   HIS B 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00703 /  0.29 (12670)
  covalent geometry    : angle       0.68708 /  0.34 (17182)
  SS BOND              : bond        0.00568 /  0.48 (   16)
  SS BOND              : angle       0.93453 /  0.60 (   32)
  hydrogen bonds       : bond        0.04304 /  2.79 (  128)
  hydrogen bonds       : angle       5.32337 /  3.64 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 122
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
REVERT: B  108 LYS cc_start: 0.0860 (OUTLIER) cc_final: 0.0050 (tppt)
REVERT: B  197 LYS cc_start: 0.8576 (tptt) cc_final: 0.8142 (ttpt)
REVERT: B  782 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6605 (m-70)
REVERT: A  197 LYS cc_start: 0.8349 (tptt) cc_final: 0.7938 (ttpt)
REVERT: A  588 MET cc_start: 0.8736 (mmm) cc_final: 0.8347 (mmm)
REVERT: A  782 HIS cc_start: 0.7056 (OUTLIER) cc_final: 0.6487 (m-70)
REVERT: A  831 TYR cc_start: 0.2119 (OUTLIER) cc_final: 0.0372 (p90)
  outliers start: 53
  outliers final: 37
  residues processed: 166
  average time/residue: 0.0896
  time to fit residues: 23.1226
Evaluate side-chains
  150 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 109
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 ILE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  800 HIS
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  640 ASN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  782 HIS
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  832 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0670
   chunk 65 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:   20.0000
   chunk 78 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 109 optimal weight:    0.6980
   overall best weight:    1.0720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 710 GLN
B 757 ASN
B 800 HIS
A 800 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.209072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.180923 restraints weight = 11869.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 1.06
r_work: 0.3639 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12686  Z= 0.121
  Angle     :  0.528   8.784  17214  Z= 0.273
  Chirality :  0.044   0.218   1974
  Planarity :  0.004   0.050   2182
  Dihedral  :  4.849  59.325   1740
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.82 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.02 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.15 (0.21), residues: 1514
  helix: -3.54 (0.38), residues: 98
  sheet: -2.78 (0.33), residues: 248
  loop : -0.95 (0.18), residues: 1168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 378 
 TYR   0.022   0.001   TYR A 233 
 PHE   0.017   0.001   PHE B 690 
 TRP   0.010   0.001   TRP A 793 
 HIS   0.014   0.001   HIS A 800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 (12670)
  covalent geometry    : angle       0.52698 /  0.27 (17182)
  SS BOND              : bond        0.00277 /  0.22 (   16)
  SS BOND              : angle       1.04456 /  0.58 (   32)
  hydrogen bonds       : bond        0.02985 /  1.91 (  128)
  hydrogen bonds       : angle       5.11842 /  3.49 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7552 (t80)
REVERT: B  108 LYS cc_start: -0.0031 (OUTLIER) cc_final: -0.0619 (tppt)
REVERT: B  197 LYS cc_start: 0.8370 (tptt) cc_final: 0.7705 (ttpt)
REVERT: B  710 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7395 (mm-40)
REVERT: A  192 SER cc_start: 0.8524 (OUTLIER) cc_final: 0.8299 (t)
REVERT: A  197 LYS cc_start: 0.8152 (tptt) cc_final: 0.7477 (ttpt)
REVERT: A  236 MET cc_start: 0.8031 (ttm) cc_final: 0.7705 (tpp)
REVERT: A  588 MET cc_start: 0.8881 (mmm) cc_final: 0.8470 (mmm)
REVERT: A  750 ARG cc_start: 0.8106 (mpt180) cc_final: 0.7548 (mpt180)
REVERT: A  831 TYR cc_start: 0.1555 (OUTLIER) cc_final: 0.0221 (p90)
  outliers start: 43
  outliers final: 31
  residues processed: 149
  average time/residue: 0.0890
  time to fit residues: 20.6121
Evaluate side-chains
  147 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 111
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  659 LYS
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  714 VAL
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  800 HIS
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 74 optimal weight:   30.0000
   chunk 136 optimal weight:   30.0000
   chunk 12 optimal weight:    6.9990
   chunk 133 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 102 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 142 optimal weight:   10.0000
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 ASN
** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 757 ASN
B 800 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.206234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.179242 restraints weight = 11945.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.05
r_work: 0.3603 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12686  Z= 0.223
  Angle     :  0.614   8.593  17214  Z= 0.312
  Chirality :  0.048   0.232   1974
  Planarity :  0.004   0.049   2182
  Dihedral  :  4.956  55.618   1739
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.34 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.88 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -2.17 (0.21), residues: 1514
  helix: -3.61 (0.35), residues: 110
  sheet: -2.87 (0.33), residues: 248
  loop : -0.90 (0.18), residues: 1156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 378 
 TYR   0.017   0.001   TYR A 233 
 PHE   0.014   0.002   PHE A 538 
 TRP   0.008   0.001   TRP A 692 
 HIS   0.015   0.001   HIS B 800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00540 /  0.22 (12670)
  covalent geometry    : angle       0.61083 /  0.31 (17182)
  SS BOND              : bond        0.00352 /  0.27 (   16)
  SS BOND              : angle       1.48964 /  0.79 (   32)
  hydrogen bonds       : bond        0.03691 /  2.39 (  128)
  hydrogen bonds       : angle       5.16652 /  3.50 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 112
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7543 (t80)
REVERT: B  108 LYS cc_start: -0.0014 (OUTLIER) cc_final: -0.0600 (tppt)
REVERT: B  197 LYS cc_start: 0.8409 (tptt) cc_final: 0.7781 (ttpt)
REVERT: B  710 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7313 (tp40)
REVERT: B  782 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6490 (m-70)
REVERT: B  799 GLN cc_start: 0.3222 (OUTLIER) cc_final: 0.2305 (tt0)
REVERT: A  192 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (t)
REVERT: A  197 LYS cc_start: 0.8290 (tptt) cc_final: 0.7677 (ttpt)
REVERT: A  588 MET cc_start: 0.8896 (mmm) cc_final: 0.8504 (mmm)
REVERT: A  750 ARG cc_start: 0.8150 (mpt180) cc_final: 0.7581 (mpt180)
REVERT: A  782 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6085 (m-70)
REVERT: A  831 TYR cc_start: 0.1785 (OUTLIER) cc_final: 0.0386 (p90)
  outliers start: 56
  outliers final: 40
  residues processed: 161
  average time/residue: 0.0893
  time to fit residues: 22.6753
Evaluate side-chains
  158 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 110
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  192 SER
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  525 SER
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  659 LYS
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  799 GLN
Chi-restraints excluded: chain B residue  800 HIS
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  192 SER
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  782 HIS
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 141 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 123 optimal weight:    0.8980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 757 ASN
B 820 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.208728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.179990 restraints weight = 11845.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 1.11
r_work: 0.3652 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12686  Z= 0.135
  Angle     :  0.533   7.581  17214  Z= 0.274
  Chirality :  0.045   0.225   1974
  Planarity :  0.004   0.049   2182
  Dihedral  :  4.716  49.749   1739
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.09 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 17.06 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    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: -2.04 (0.21), residues: 1514
  helix: -3.48 (0.36), residues: 110
  sheet: -2.83 (0.33), residues: 248
  loop : -0.79 (0.18), residues: 1156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 378 
 TYR   0.020   0.001   TYR A 233 
 PHE   0.014   0.002   PHE B 506 
 TRP   0.010   0.001   TRP B 793 
 HIS   0.007   0.001   HIS B 800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 (12670)
  covalent geometry    : angle       0.53118 /  0.27 (17182)
  SS BOND              : bond        0.00215 /  0.16 (   16)
  SS BOND              : angle       1.10282 /  0.62 (   32)
  hydrogen bonds       : bond        0.02992 /  1.93 (  128)
  hydrogen bonds       : angle       5.05235 /  3.41 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 117
  time to evaluate  : 0.470 
Fit side-chains
REVERT: B   96 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7180 (t80)
REVERT: B  108 LYS cc_start: 0.0480 (OUTLIER) cc_final: -0.0190 (tppt)
REVERT: B  197 LYS cc_start: 0.8383 (tptt) cc_final: 0.7928 (ttpt)
REVERT: B  710 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7305 (mm-40)
REVERT: B  782 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6378 (m-70)
REVERT: B  799 GLN cc_start: 0.3441 (OUTLIER) cc_final: 0.2669 (tt0)
REVERT: A  197 LYS cc_start: 0.8218 (tptt) cc_final: 0.7790 (ttpt)
REVERT: A  588 MET cc_start: 0.8652 (mmm) cc_final: 0.8325 (mmm)
REVERT: A  831 TYR cc_start: 0.1869 (OUTLIER) cc_final: 0.0072 (p90)
  outliers start: 45
  outliers final: 35
  residues processed: 155
  average time/residue: 0.0830
  time to fit residues: 20.2093
Evaluate side-chains
  151 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 110
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  799 GLN
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  820 HIS
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue  108 LYS
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 133 optimal weight:    5.9990
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 92 optimal weight:    0.6980
   chunk 141 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   chunk 99 optimal weight:    0.5980
   chunk 113 optimal weight:    4.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 710 GLN
B 820 HIS
A 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.210051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.184085 restraints weight = 11832.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.07
r_work: 0.3691 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  12686  Z= 0.103
  Angle     :  0.511   7.397  17214  Z= 0.264
  Chirality :  0.044   0.211   1974
  Planarity :  0.004   0.050   2182
  Dihedral  :  4.558  45.527   1739
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.15 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 17.48 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    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: -1.86 (0.22), residues: 1514
  helix: -3.34 (0.40), residues: 98
  sheet: -2.60 (0.31), residues: 284
  loop : -0.65 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 750 
 TYR   0.020   0.001   TYR A 233 
 PHE   0.013   0.001   PHE B 506 
 TRP   0.010   0.001   TRP B 793 
 HIS   0.007   0.001   HIS B 820 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 (12670)
  covalent geometry    : angle       0.51043 /  0.26 (17182)
  SS BOND              : bond        0.00168 /  0.12 (   16)
  SS BOND              : angle       0.90471 /  0.54 (   32)
  hydrogen bonds       : bond        0.02657 /  1.71 (  128)
  hydrogen bonds       : angle       4.95584 /  3.34 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 108
  time to evaluate  : 0.352 
Fit side-chains
REVERT: B   96 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7455 (t80)
REVERT: B  108 LYS cc_start: 0.0269 (OUTLIER) cc_final: -0.0374 (tppt)
REVERT: B  197 LYS cc_start: 0.8466 (tptt) cc_final: 0.7881 (ttpt)
REVERT: B  710 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7441 (mm-40)
REVERT: A  197 LYS cc_start: 0.8340 (tptt) cc_final: 0.7801 (ttpt)
REVERT: A  588 MET cc_start: 0.8836 (mmm) cc_final: 0.8459 (mmm)
REVERT: A  831 TYR cc_start: 0.1865 (OUTLIER) cc_final: 0.0289 (p90)
  outliers start: 47
  outliers final: 39
  residues processed: 149
  average time/residue: 0.0843
  time to fit residues: 20.0367
Evaluate side-chains
  149 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 106
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  659 LYS
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  820 HIS
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue  108 LYS
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 100 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 128 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 132 optimal weight:    5.9990
   chunk 149 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 800 HIS
B 820 HIS
A 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.207791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.179134 restraints weight = 11960.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.14
r_work: 0.3633 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12686  Z= 0.144
  Angle     :  0.535   7.690  17214  Z= 0.275
  Chirality :  0.045   0.232   1974
  Planarity :  0.004   0.048   2182
  Dihedral  :  4.597  41.079   1739
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.75 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.41 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    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: -1.82 (0.22), residues: 1514
  helix: -3.29 (0.41), residues: 98
  sheet: -2.64 (0.31), residues: 286
  loop : -0.59 (0.19), residues: 1130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 378 
 TYR   0.017   0.001   TYR A 233 
 PHE   0.014   0.002   PHE B 506 
 TRP   0.009   0.001   TRP B 793 
 HIS   0.006   0.001   HIS B 820 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.14 (12670)
  covalent geometry    : angle       0.53382 /  0.27 (17182)
  SS BOND              : bond        0.00224 /  0.17 (   16)
  SS BOND              : angle       1.08584 /  0.62 (   32)
  hydrogen bonds       : bond        0.02901 /  1.89 (  128)
  hydrogen bonds       : angle       4.95803 /  3.34 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 113
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7276 (t80)
REVERT: B  108 LYS cc_start: 0.0454 (OUTLIER) cc_final: -0.0186 (tppt)
REVERT: B  197 LYS cc_start: 0.8375 (tptt) cc_final: 0.7913 (ttpt)
REVERT: B  782 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6358 (m-70)
REVERT: A  197 LYS cc_start: 0.8239 (tptt) cc_final: 0.7841 (ttpt)
REVERT: A  588 MET cc_start: 0.8664 (mmm) cc_final: 0.8351 (mmm)
REVERT: A  782 HIS cc_start: 0.6944 (OUTLIER) cc_final: 0.6082 (m-70)
REVERT: A  831 TYR cc_start: 0.2057 (OUTLIER) cc_final: 0.0261 (p90)
  outliers start: 50
  outliers final: 40
  residues processed: 157
  average time/residue: 0.0918
  time to fit residues: 23.0248
Evaluate side-chains
  153 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 108
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 LYS
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  298 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  800 HIS
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  298 HIS
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  782 HIS
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 139 optimal weight:    8.9990
   chunk 124 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 123 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 167 GLN
B 757 ASN
B 800 HIS
A 300 ASN
A 820 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.203724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.173677 restraints weight = 11908.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 1.13
r_work: 0.3583 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12686  Z= 0.239
  Angle     :  0.627   8.722  17214  Z= 0.318
  Chirality :  0.048   0.234   1974
  Planarity :  0.004   0.047   2182
  Dihedral  :  4.855  34.733   1739
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  6.87 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.04 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.92 (0.22), residues: 1514
  helix: -3.42 (0.39), residues: 108
  sheet: -2.73 (0.31), residues: 286
  loop : -0.61 (0.19), residues: 1120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 378 
 TYR   0.015   0.002   TYR A 492 
 PHE   0.017   0.002   PHE B 351 
 TRP   0.009   0.001   TRP A 692 
 HIS   0.016   0.001   HIS B 800 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.24 (12670)
  covalent geometry    : angle       0.62413 /  0.32 (17182)
  SS BOND              : bond        0.00357 /  0.27 (   16)
  SS BOND              : angle       1.48309 /  0.81 (   32)
  hydrogen bonds       : bond        0.03649 /  2.39 (  128)
  hydrogen bonds       : angle       5.10782 /  3.45 (  234)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 110
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: B   96 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7397 (t80)
REVERT: B  111 MET cc_start: 0.2580 (ttt) cc_final: 0.2044 (ttt)
REVERT: B  197 LYS cc_start: 0.8390 (tptt) cc_final: 0.7914 (ttpt)
REVERT: B  782 HIS cc_start: 0.7112 (OUTLIER) cc_final: 0.6351 (m-70)
REVERT: A  197 LYS cc_start: 0.8277 (tptt) cc_final: 0.7848 (ttpt)
REVERT: A  588 MET cc_start: 0.8694 (mmm) cc_final: 0.8381 (mmm)
REVERT: A  782 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6121 (m-70)
REVERT: A  831 TYR cc_start: 0.2029 (OUTLIER) cc_final: 0.0341 (p90)
  outliers start: 45
  outliers final: 39
  residues processed: 150
  average time/residue: 0.0921
  time to fit residues: 22.0269
Evaluate side-chains
  148 residues out of total 1436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 105
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  276 ASN
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  430 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  659 LYS
Chi-restraints excluded: chain B residue  710 GLN
Chi-restraints excluded: chain B residue  759 ILE
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain B residue  783 ASN
Chi-restraints excluded: chain B residue  800 HIS
Chi-restraints excluded: chain B residue  810 THR
Chi-restraints excluded: chain B residue  812 VAL
Chi-restraints excluded: chain B residue  825 VAL
Chi-restraints excluded: chain B residue  831 TYR
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  300 ASN
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  586 THR
Chi-restraints excluded: chain A residue  724 SER
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  782 HIS
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  820 HIS
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  828 LEU
Chi-restraints excluded: chain A residue  831 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 76 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 110 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  99 ASN
B 275 ASN
B 757 ASN
B 800 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.208312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.180305 restraints weight = 11784.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 1.15
r_work: 0.3636 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12686  Z= 0.127
  Angle     :  0.542   7.689  17214  Z= 0.277
  Chirality :  0.045   0.224   1974
  Planarity :  0.004   0.049   2182
  Dihedral  :  4.630  27.719   1739
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.22 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.45 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.14 %
    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: -1.81 (0.22), residues: 1514
  helix: -3.37 (0.38), residues: 108
  sheet: -2.68 (0.31), residues: 286
  loop : -0.52 (0.19), residues: 1120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 378 
 TYR   0.020   0.001   TYR A 233 
 PHE   0.014   0.002   PHE B 161 
 TRP   0.010   0.001   TRP B 793 
 HIS   0.004   0.001   HIS B 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 (12670)
  covalent geometry    : angle       0.53965 /  0.28 (17182)
  SS BOND              : bond        0.00223 /  0.17 (   16)
  SS BOND              : angle       1.27323 /  0.69 (   32)
  hydrogen bonds       : bond        0.02854 /  1.86 (  128)
  hydrogen bonds       : angle       4.97312 /  3.35 (  234)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2556.46 seconds
wall clock time: 44 minutes 45.69 seconds (2685.69 seconds total)