Starting phenix.real_space_refine
on Thu Jul  2 12:01:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rz9_19607/07_2026/8rz9_19607.map"
  }
  resolution = 3.02
  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=   0.001 sd=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      44      5.16       5
     C    5433      2.51       5
     N    1470      2.21       5
     O    1616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  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: 8571
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4232
          Classifications: {'peptide': 534}
          Link IDs: {'PTRANS': 16, 'TRANS': 517}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4275
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4275
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 15, 'TRANS': 517}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   THR A 320 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR A 320 " occ=0.00
    residue:
      pdb=" N   GLY A 322 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A 322 " occ=0.00
    residue:
      pdb=" N   SER A 323 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OG  SER A 323 " occ=0.00
  Time building chain proxies: 1.78, per 1000 atoms: 0.21
  Number of scatterers: 8571
  At special positions: 0
  Unit cell: (74.9644, 106.047, 146.272, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      44     16.00
     P       6     15.00
     Mg      2     11.99
     O    1616      8.00
     N    1470      7.00
     C    5433      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 454.7 milliseconds
  

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      60.4% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 325 through 331
    Processing helix  chain 'A' and resid 335 through 348
    Processing helix  chain 'A' and resid 352 through 369
      removed outlier: 3.590A  pdb=" N   ILE A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 378
      removed outlier: 3.611A  pdb=" N   ARG A 373 " --> pdb=" O   ASP A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 400 through 424
      Proline residue:  A 415  - end of helix
    Processing helix  chain 'A' and resid 429 through 457
      Proline residue:  A 439  - end of helix
      removed outlier: 4.808A  pdb=" N   LYS A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   PHE A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 503
    Processing helix  chain 'A' and resid 553 through 586
      removed outlier: 3.772A  pdb=" N   GLU A 569 " --> pdb=" O   LYS A 565 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   GLU A 580 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ASN A 583 " --> pdb=" O   LYS A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 615
      removed outlier: 3.654A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 692
      removed outlier: 3.746A  pdb=" N   GLY A 692 " --> pdb=" O   MET A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 739
      removed outlier: 3.798A  pdb=" N   THR A 732 " --> pdb=" O   GLU A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 773
    Processing helix  chain 'A' and resid 786 through 788
      No H-bonds generated for 'chain 'A' and resid 786 through 788'
    Processing helix  chain 'A' and resid 789 through 794
    Processing helix  chain 'A' and resid 826 through 834
      removed outlier: 3.512A  pdb=" N   VAL A 830 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 851
    Processing helix  chain 'A' and resid 852 through 855
      removed outlier: 3.774A  pdb=" N   GLN A 855 " --> pdb=" O   GLU A 852 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 852 through 855'
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 559 through 565
      removed outlier: 3.565A  pdb=" N   VAL B 563 " --> pdb=" O   SER B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 582
    Processing helix  chain 'B' and resid 586 through 602
      removed outlier: 3.941A  pdb=" N   ILE B 590 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 616
    Processing helix  chain 'B' and resid 620 through 630
      removed outlier: 3.686A  pdb=" N   GLY B 624 " --> pdb=" O   ASP B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 655
      removed outlier: 3.651A  pdb=" N   VAL B 642 " --> pdb=" O   PHE B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 660
    Processing helix  chain 'B' and resid 665 through 679
      Proline residue:  B 676  - end of helix
    Processing helix  chain 'B' and resid 681 through 689
      removed outlier: 4.058A  pdb=" N   TYR B 685 " --> pdb=" O   PRO B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 697
      removed outlier: 3.802A  pdb=" N   ALA B 694 " --> pdb=" O   ASN B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 708
    Processing helix  chain 'B' and resid 709 through 737
      removed outlier: 4.067A  pdb=" N   ARG B 715 " --> pdb=" O   LEU B 711 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLN B 731 " --> pdb=" O   ARG B 727 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   GLU B 732 " --> pdb=" O   MET B 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 816
    Processing helix  chain 'B' and resid 817 through 844
      removed outlier: 3.857A  pdb=" N   VAL B 825 " --> pdb=" O   LEU B 821 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY B 844 " --> pdb=" O   VAL B 840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 864 through 872
    Processing helix  chain 'B' and resid 897 through 900
    Processing helix  chain 'B' and resid 901 through 919
    Processing helix  chain 'B' and resid 950 through 966
    Processing helix  chain 'B' and resid 982 through 1000
    Processing helix  chain 'B' and resid 1011 through 1016
      removed outlier: 4.126A  pdb=" N   CYS B1015 " --> pdb=" O   TYR B1011 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLU B1016 " --> pdb=" O   PRO B1012 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1011 through 1016'
    Processing helix  chain 'B' and resid 1016 through 1021
      removed outlier: 4.271A  pdb=" N   ASN B1020 " --> pdb=" O   GLU B1016 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1068 through 1076
    Processing helix  chain 'B' and resid 1079 through 1103
    Processing sheet with id=AA1, first strand: chain 'A' and resid 512 through 513
    Processing sheet with id=AA2, first strand: chain 'A' and resid 653 through 656
      removed outlier: 7.013A  pdb=" N   VAL A 655 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   LYS A 635 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.482A  pdb=" N   LEU A 709 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   HIS A 665 " --> pdb=" O   PHE A 780 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   PHE A 664 " --> pdb=" O   ASN A 798 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU A 800 " --> pdb=" O   PHE A 664 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   ILE A 666 " --> pdb=" O   LEU A 800 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   VAL A 802 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   THR A 668 " --> pdb=" O   VAL A 802 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   ALA A 804 " --> pdb=" O   THR A 668 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ASN A 799 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   LYS A 818 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   HIS A 801 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   GLN A 816 " --> pdb=" O   HIS A 801 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   THR A 803 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 769 through 772
      removed outlier: 6.966A  pdb=" N   ARG B 779 " --> pdb=" O   VAL B 771 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 880 through 885
      removed outlier: 4.978A  pdb=" N   ASN B 880 " --> pdb=" O   ASN B 861 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ASN B 861 " --> pdb=" O   ASN B 880 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 935 through 938
      removed outlier: 6.050A  pdb=" N   PHE B 936 " --> pdb=" O   ILE B 973 " (cutoff:3.500A)
      removed outlier: 7.648A  pdb=" N   ASP B 975 " --> pdb=" O   PHE B 936 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ARG B 938 " --> pdb=" O   ASP B 975 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   VAL B 972 " --> pdb=" O   LEU B1006 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   VAL B1008 " --> pdb=" O   VAL B 972 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   LEU B 974 " --> pdb=" O   VAL B1008 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   GLN B1058 " --> pdb=" O   GLY B1031 " (cutoff:3.500A)
      removed outlier: 8.787A  pdb=" N   LEU B1033 " --> pdb=" O   LEU B1056 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   LEU B1056 " --> pdb=" O   LEU B1033 " (cutoff:3.500A)

    477 hydrogen bonds defined for protein.
    1404 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.19 -     1.34: 2580
        1.34 -     1.49: 2293
        1.49 -     1.63: 3773
        1.63 -     1.78: 2
        1.78 -     1.93: 68
  Bond restraints: 8716
  Sorted by residual:
  bond pdb=" CD  ARG A 382 "
       pdb=" NE  ARG A 382 "
    ideal  model  delta    sigma   weight residual
    1.458  1.602 -0.144 1.40e-02 5.10e+03 1.05e+02
  bond pdb=" C   ASP A 319 "
       pdb=" N   THR A 320 "
    ideal  model  delta    sigma   weight residual
    1.331  1.194  0.137 1.41e-02 5.03e+03 9.44e+01
  bond pdb=" CA  LYS B1102 "
       pdb=" CB  LYS B1102 "
    ideal  model  delta    sigma   weight residual
    1.528  1.387  0.142 1.56e-02 4.11e+03 8.25e+01
  bond pdb=" CA  SER B1090 "
       pdb=" CB  SER B1090 "
    ideal  model  delta    sigma   weight residual
    1.529  1.401  0.128 1.55e-02 4.16e+03 6.85e+01
  bond pdb=" CA  ASP B 705 "
       pdb=" CB  ASP B 705 "
    ideal  model  delta    sigma   weight residual
    1.523  1.425  0.099 1.27e-02 6.20e+03 6.03e+01
  ... (remaining 8711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11067
        2.32 -     4.64: 630
        4.64 -     6.96: 60
        6.96 -     9.27: 9
        9.27 -    11.59: 7
  Bond angle restraints: 11773
  Sorted by residual:
  angle pdb=" N   ILE B 675 "
        pdb=" CA  ILE B 675 "
        pdb=" CB  ILE B 675 "
      ideal   model   delta    sigma   weight residual
     110.45  115.37   -4.92 7.80e-01 1.64e+00 3.97e+01
  angle pdb=" CB  GLU A 647 "
        pdb=" CG  GLU A 647 "
        pdb=" CD  GLU A 647 "
      ideal   model   delta    sigma   weight residual
     112.60  122.37   -9.77 1.70e+00 3.46e-01 3.30e+01
  angle pdb=" OD1 ASN B1071 "
        pdb=" CG  ASN B1071 "
        pdb=" ND2 ASN B1071 "
      ideal   model   delta    sigma   weight residual
     122.60  116.86    5.74 1.00e+00 1.00e+00 3.29e+01
  angle pdb=" N   LYS B 947 "
        pdb=" CA  LYS B 947 "
        pdb=" CB  LYS B 947 "
      ideal   model   delta    sigma   weight residual
     110.73  119.58   -8.85 1.55e+00 4.16e-01 3.26e+01
  angle pdb=" CA  ASP A 646 "
        pdb=" CB  ASP A 646 "
        pdb=" CG  ASP A 646 "
      ideal   model   delta    sigma   weight residual
     112.60  107.71    4.89 1.00e+00 1.00e+00 2.39e+01
  ... (remaining 11768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.56: 4973
       28.56 -    57.12: 351
       57.12 -    85.68: 28
       85.68 -   114.23: 1
      114.23 -   142.79: 4
  Dihedral angle restraints: 5357
    sinusoidal: 2239
      harmonic: 3118
  Sorted by residual:
  dihedral pdb=" N   ASN B 788 "
           pdb=" C   ASN B 788 "
           pdb=" CA  ASN B 788 "
           pdb=" CB  ASN B 788 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.09  -12.29     0      2.50e+00 1.60e-01 2.42e+01
  dihedral pdb=" C   ASN B 788 "
           pdb=" N   ASN B 788 "
           pdb=" CA  ASN B 788 "
           pdb=" CB  ASN B 788 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.11   11.51     0      2.50e+00 1.60e-01 2.12e+01
  dihedral pdb=" C   ASP B1000 "
           pdb=" N   ASP B1000 "
           pdb=" CA  ASP B1000 "
           pdb=" CB  ASP B1000 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.87   11.27     0      2.50e+00 1.60e-01 2.03e+01
  ... (remaining 5354 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1034
       0.105 -    0.209: 279
       0.209 -    0.314: 29
       0.314 -    0.418: 4
       0.418 -    0.523: 7
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CA  ASN B 788 "
            pdb=" N   ASN B 788 "
            pdb=" C   ASN B 788 "
            pdb=" CB  ASN B 788 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.83e+00
  chirality pdb=" CA  LYS B1102 "
            pdb=" N   LYS B1102 "
            pdb=" C   LYS B1102 "
            pdb=" CB  LYS B1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.91e+00
  chirality pdb=" CA  SER B1090 "
            pdb=" N   SER B1090 "
            pdb=" C   SER B1090 "
            pdb=" CB  SER B1090 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.47e+00
  ... (remaining 1350 not shown)

  Planarity restraints: 1489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 382 "    0.321 9.50e-02 1.11e+02   1.44e-01 1.28e+01
        pdb=" NE  ARG A 382 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 382 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 382 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 382 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 308 "    0.202 9.50e-02 1.11e+02   9.36e-02 1.25e+01
        pdb=" NE  ARG A 308 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 308 "    0.045 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 308 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 308 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 323 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   SER A 323 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   SER A 323 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A 324 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1486 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.33: 25
        2.33 -     2.97: 4282
        2.97 -     3.61: 13759
        3.61 -     4.26: 20315
        4.26 -     4.90: 33904
  Nonbonded interactions: 72285
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 898 "
            pdb=" O3B AGS B2001 "
     model   vdw
     1.685 3.040
  nonbonded pdb=" OG  SER A 676 "
            pdb="MG    MG A2000 "
     model   vdw
     1.752 2.170
  nonbonded pdb=" ND2 ASN A 311 "
            pdb=" OH  TYR B 946 "
     model   vdw
     1.930 3.120
  nonbonded pdb=" OD2 ASP A 369 "
            pdb=" ND1 HIS A 424 "
     model   vdw
     2.059 3.120
  nonbonded pdb=" O   MET B 728 "
            pdb=" OE1 GLU B 732 "
     model   vdw
     2.082 3.040
  ... (remaining 72280 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.00 max=1.00 mean=0.90
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.850
  Find NCS groups from input model:        0.040
  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:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
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      :  0.015   0.781   8718  Z= 1.266
  Angle     :  1.276  11.594  11773  Z= 0.831
  Chirality :  0.096   0.523   1353
  Planarity :  0.007   0.144   1489
  Dihedral  : 18.107 142.792   3329
  Min Nonbonded Distance : 1.685

Molprobity Statistics.
  All-atom Clashscore : 25.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.25 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.39 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.24), residues: 1049
  helix: -0.15 (0.20), residues: 597
  sheet: -2.23 (0.47), residues: 99
  loop : -2.39 (0.30), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.050   0.002   ARG B 573 
 TYR   0.029   0.004   TYR A 570 
 PHE   0.019   0.004   PHE B 936 
 TRP   0.017   0.004   TRP B 562 
 HIS   0.016   0.002   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01054 /  0.62 ( 8716)
  covalent geometry    : angle       1.27563 /  0.83 (11773)
  hydrogen bonds       : bond        0.15434 / 10.59 (  477)
  hydrogen bonds       : angle       7.01008 /  4.79 ( 1404)
  Misc. bond           : bond        0.72766 / 36.79 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 218
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  300 MET cc_start: 0.7929 (ttm) cc_final: 0.7458 (ttm)
REVERT: A  301 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7567 (mppt)
REVERT: A  384 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7947 (m-80)
REVERT: A  691 ILE cc_start: 0.8075 (mm) cc_final: 0.7740 (mm)
REVERT: B  553 ASP cc_start: 0.7911 (t0) cc_final: 0.7262 (t0)
REVERT: B  555 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7361 (mtmm)
REVERT: B  589 GLU cc_start: 0.8798 (mp0) cc_final: 0.8428 (pm20)
REVERT: B  688 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: B  702 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7365 (tt)
  outliers start: 34
  outliers final: 14
  residues processed: 239
  average time/residue: 0.1017
  time to fit residues: 32.2000
Evaluate side-chains
  225 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 207
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 LYS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain B residue  542 LEU
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  702 LEU
Chi-restraints excluded: chain B residue  779 ARG
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue  999 ARG
Chi-restraints excluded: chain B residue 1033 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 ASN
B 684 HIS
B 827 HIS
B 944 ASN
B1088 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.159171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.140579 restraints weight = 12609.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 2.04
r_work: 0.3872 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8718  Z= 0.193
  Angle     :  0.665  13.093  11773  Z= 0.348
  Chirality :  0.044   0.213   1353
  Planarity :  0.004   0.039   1489
  Dihedral  : 12.164 158.610   1255
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 24.31 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.26), residues: 1049
  helix:  0.66 (0.21), residues: 602
  sheet: -2.20 (0.47), residues: 97
  loop : -1.97 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 638 
 TYR   0.022   0.002   TYR A 769 
 PHE   0.010   0.002   PHE B 952 
 TRP   0.014   0.002   TRP B 562 
 HIS   0.013   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.19 ( 8716)
  covalent geometry    : angle       0.66541 /  0.35 (11773)
  hydrogen bonds       : bond        0.05188 /  3.39 (  477)
  hydrogen bonds       : angle       5.31754 /  3.63 ( 1404)
  Misc. bond           : bond        0.00291 /  0.14 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 213
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: A  592 MET cc_start: 0.8345 (tmm) cc_final: 0.8024 (ptp)
REVERT: A  629 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6940 (mp10)
REVERT: B  553 ASP cc_start: 0.7573 (t0) cc_final: 0.7257 (t0)
REVERT: B  688 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7334 (mp)
REVERT: B  729 HIS cc_start: 0.7240 (t-170) cc_final: 0.6957 (t-170)
REVERT: B  839 LYS cc_start: 0.8294 (tppp) cc_final: 0.7896 (tttm)
  outliers start: 48
  outliers final: 26
  residues processed: 240
  average time/residue: 0.1109
  time to fit residues: 35.3943
Evaluate side-chains
  233 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 205
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  339 GLN
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  799 ASN
Chi-restraints excluded: chain A residue  802 VAL
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  648 LEU
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  840 VAL
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1066 ARG
Chi-restraints excluded: chain B residue 1072 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 94 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 566 ASN
A 613 ASN
B 684 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.158041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.139872 restraints weight = 12453.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 2.03
r_work: 0.3861 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8718  Z= 0.206
  Angle     :  0.642  12.881  11773  Z= 0.336
  Chirality :  0.045   0.242   1353
  Planarity :  0.004   0.055   1489
  Dihedral  : 11.341 159.001   1229
  Min Nonbonded Distance : 1.760

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 23.99 %
    Favored  : 70.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.69 (0.26), residues: 1049
  helix:  0.69 (0.21), residues: 602
  sheet: -2.22 (0.46), residues: 97
  loop : -1.89 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 779 
 TYR   0.023   0.002   TYR A 769 
 PHE   0.019   0.002   PHE B1007 
 TRP   0.009   0.002   TRP B 562 
 HIS   0.005   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.21 ( 8716)
  covalent geometry    : angle       0.64214 /  0.34 (11773)
  hydrogen bonds       : bond        0.04957 /  3.26 (  477)
  hydrogen bonds       : angle       5.07510 /  3.50 ( 1404)
  Misc. bond           : bond        0.00258 /  0.12 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 213
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7607 (t0) cc_final: 0.7401 (t0)
REVERT: A  344 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7423 (tm-30)
REVERT: A  369 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5914 (m-30)
REVERT: A  592 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8056 (ptp)
REVERT: A  629 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7009 (mp10)
REVERT: A  638 ARG cc_start: 0.6612 (ptt90) cc_final: 0.6401 (ptp90)
REVERT: A  778 CYS cc_start: 0.8106 (t) cc_final: 0.7883 (t)
REVERT: B  688 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7135 (mp)
REVERT: B  729 HIS cc_start: 0.7274 (t-170) cc_final: 0.6901 (t-170)
REVERT: B  839 LYS cc_start: 0.8342 (tppp) cc_final: 0.8082 (tttm)
REVERT: B  889 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6566 (mt-10)
REVERT: B 1061 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7438 (ttm-80)
  outliers start: 55
  outliers final: 36
  residues processed: 244
  average time/residue: 0.1094
  time to fit residues: 35.6697
Evaluate side-chains
  246 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 206
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  799 ASN
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  840 VAL
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1066 ARG
Chi-restraints excluded: chain B residue 1072 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0970
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 348 GLN
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 944 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.157731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.139323 restraints weight = 12665.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 2.07
r_work: 0.3853 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8718  Z= 0.210
  Angle     :  0.649  12.279  11773  Z= 0.337
  Chirality :  0.045   0.225   1353
  Planarity :  0.005   0.049   1489
  Dihedral  : 11.233 162.274   1227
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 25.69 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.26), residues: 1049
  helix:  0.65 (0.21), residues: 602
  sheet: -2.16 (0.46), residues: 99
  loop : -1.78 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 711 
 TYR   0.024   0.002   TYR A 769 
 PHE   0.010   0.001   PHE B 652 
 TRP   0.011   0.002   TRP B 807 
 HIS   0.004   0.001   HIS B 984 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.21 ( 8716)
  covalent geometry    : angle       0.64941 /  0.34 (11773)
  hydrogen bonds       : bond        0.04743 /  3.10 (  477)
  hydrogen bonds       : angle       4.97254 /  3.43 ( 1404)
  Misc. bond           : bond        0.00235 /  0.11 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 210
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7702 (t0) cc_final: 0.7359 (t0)
REVERT: A  369 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5729 (m-30)
REVERT: A  584 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7057 (tp)
REVERT: A  592 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8065 (ptp)
REVERT: A  629 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7104 (mp10)
REVERT: A  691 ILE cc_start: 0.7851 (mt) cc_final: 0.7599 (mt)
REVERT: A  778 CYS cc_start: 0.8142 (t) cc_final: 0.7923 (t)
REVERT: B  555 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7709 (ptpp)
REVERT: B  628 ILE cc_start: 0.8190 (mt) cc_final: 0.7925 (mt)
REVERT: B  688 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7015 (mp)
REVERT: B  729 HIS cc_start: 0.7565 (t-170) cc_final: 0.7157 (t-170)
REVERT: B  839 LYS cc_start: 0.8346 (tppp) cc_final: 0.8068 (tttm)
REVERT: B  889 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: B  917 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (mt0)
REVERT: B 1084 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7677 (mtpp)
  outliers start: 58
  outliers final: 36
  residues processed: 242
  average time/residue: 0.1079
  time to fit residues: 35.1290
Evaluate side-chains
  247 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 205
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0170
   chunk 34 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 ASN
B 731 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.159174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.140828 restraints weight = 12549.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 2.06
r_work: 0.3876 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3730 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8718  Z= 0.159
  Angle     :  0.612  11.890  11773  Z= 0.315
  Chirality :  0.043   0.243   1353
  Planarity :  0.004   0.044   1489
  Dihedral  : 10.946 163.810   1227
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 26.86 %
    Favored  : 67.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.26), residues: 1049
  helix:  0.80 (0.21), residues: 603
  sheet: -1.91 (0.49), residues: 92
  loop : -1.71 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 638 
 TYR   0.018   0.001   TYR A 769 
 PHE   0.023   0.001   PHE B1007 
 TRP   0.007   0.001   TRP B 562 
 HIS   0.004   0.001   HIS B 984 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8716)
  covalent geometry    : angle       0.61245 /  0.32 (11773)
  hydrogen bonds       : bond        0.04461 /  2.93 (  477)
  hydrogen bonds       : angle       4.84958 /  3.35 ( 1404)
  Misc. bond           : bond        0.00190 /  0.09 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 204
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7658 (t0) cc_final: 0.7220 (t0)
REVERT: A  369 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5939 (m-30)
REVERT: A  562 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6706 (mt-10)
REVERT: A  584 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.7027 (tp)
REVERT: A  592 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8085 (ptt)
REVERT: A  629 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7061 (mp10)
REVERT: A  691 ILE cc_start: 0.7948 (mt) cc_final: 0.7666 (mt)
REVERT: B  555 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7854 (ptpp)
REVERT: B  628 ILE cc_start: 0.8199 (mt) cc_final: 0.7928 (mt)
REVERT: B  688 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7053 (mp)
REVERT: B  839 LYS cc_start: 0.8345 (tppp) cc_final: 0.8097 (tttm)
REVERT: B  889 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6928 (mt-10)
REVERT: B  917 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8374 (mt0)
REVERT: B 1084 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7668 (mtpp)
  outliers start: 57
  outliers final: 41
  residues processed: 238
  average time/residue: 0.1073
  time to fit residues: 34.3035
Evaluate side-chains
  240 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 192
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  799 ASN
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  594 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1066 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 76 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0970
   chunk 64 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 53 optimal weight:    0.2980
   chunk 73 optimal weight:    8.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN
B 731 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.159554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.141294 restraints weight = 12606.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.07
r_work: 0.3885 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8718  Z= 0.154
  Angle     :  0.614  10.879  11773  Z= 0.316
  Chirality :  0.044   0.233   1353
  Planarity :  0.004   0.044   1489
  Dihedral  : 10.896 165.061   1227
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 27.60 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1049
  helix:  0.82 (0.21), residues: 603
  sheet: -1.98 (0.46), residues: 104
  loop : -1.65 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.019   0.001   TYR B 629 
 PHE   0.009   0.001   PHE B 652 
 TRP   0.005   0.001   TRP B 562 
 HIS   0.017   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 ( 8716)
  covalent geometry    : angle       0.61357 /  0.32 (11773)
  hydrogen bonds       : bond        0.04387 /  2.88 (  477)
  hydrogen bonds       : angle       4.80410 /  3.32 ( 1404)
  Misc. bond           : bond        0.00182 /  0.09 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 203
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7639 (t0) cc_final: 0.7199 (t0)
REVERT: A  344 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7512 (tm-30)
REVERT: A  369 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5808 (m-30)
REVERT: A  562 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6623 (mt-10)
REVERT: A  592 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8097 (ptt)
REVERT: A  629 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7043 (mp10)
REVERT: A  691 ILE cc_start: 0.7947 (mt) cc_final: 0.7615 (mt)
REVERT: B  533 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7583 (mm-30)
REVERT: B  555 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7708 (ptpp)
REVERT: B  589 GLU cc_start: 0.8285 (pm20) cc_final: 0.7961 (pm20)
REVERT: B  628 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7911 (mt)
REVERT: B  688 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7052 (mp)
REVERT: B  839 LYS cc_start: 0.8353 (tppp) cc_final: 0.8114 (tttm)
REVERT: B  889 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6128 (mt-10)
REVERT: B  917 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8383 (mt0)
REVERT: B 1084 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7591 (mtpp)
  outliers start: 60
  outliers final: 43
  residues processed: 240
  average time/residue: 0.1031
  time to fit residues: 33.2762
Evaluate side-chains
  251 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 201
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain A residue  799 ASN
Chi-restraints excluded: chain A residue  800 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  628 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1005 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Chi-restraints excluded: chain B residue 1075 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 96 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 95 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0070
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 551 GLN
B 660 ASN
B 731 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.159489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.141161 restraints weight = 12688.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 2.10
r_work: 0.3879 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8718  Z= 0.159
  Angle     :  0.617   9.827  11773  Z= 0.318
  Chirality :  0.044   0.320   1353
  Planarity :  0.004   0.045   1489
  Dihedral  : 10.901 164.875   1227
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 27.07 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.37 (0.26), residues: 1049
  helix:  0.87 (0.21), residues: 600
  sheet: -1.92 (0.47), residues: 104
  loop : -1.62 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.018   0.001   TYR A 769 
 PHE   0.009   0.001   PHE B 652 
 TRP   0.004   0.001   TRP A 345 
 HIS   0.019   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 8716)
  covalent geometry    : angle       0.61688 /  0.32 (11773)
  hydrogen bonds       : bond        0.04370 /  2.86 (  477)
  hydrogen bonds       : angle       4.81584 /  3.34 ( 1404)
  Misc. bond           : bond        0.00187 /  0.09 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 202
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7703 (t0) cc_final: 0.7237 (t0)
REVERT: A  344 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7458 (tm-30)
REVERT: A  369 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5758 (m-30)
REVERT: A  562 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6572 (mt-10)
REVERT: A  584 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7008 (tp)
REVERT: A  592 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8107 (ptt)
REVERT: A  629 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7060 (mp10)
REVERT: A  691 ILE cc_start: 0.7948 (mt) cc_final: 0.7602 (mt)
REVERT: B  555 LYS cc_start: 0.8103 (ptpp) cc_final: 0.7720 (ptpp)
REVERT: B  628 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7937 (mt)
REVERT: B  688 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7044 (mp)
REVERT: B  839 LYS cc_start: 0.8346 (tppp) cc_final: 0.8047 (tttm)
REVERT: B  889 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6777 (mt-10)
REVERT: B  917 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8396 (mt0)
REVERT: B  994 LEU cc_start: 0.6489 (tp) cc_final: 0.5556 (tp)
REVERT: B 1084 LYS cc_start: 0.7914 (ttmm) cc_final: 0.7613 (mtpp)
  outliers start: 64
  outliers final: 44
  residues processed: 242
  average time/residue: 0.1092
  time to fit residues: 35.3314
Evaluate side-chains
  249 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 197
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  728 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  628 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  702 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1005 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 89 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9990
   chunk 78 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 GLN
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.159287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.141163 restraints weight = 12378.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 2.05
r_work: 0.3880 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8718  Z= 0.172
  Angle     :  0.636  10.754  11773  Z= 0.327
  Chirality :  0.045   0.268   1353
  Planarity :  0.004   0.045   1489
  Dihedral  : 10.885 164.568   1225
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 27.71 %
    Favored  : 65.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1049
  helix:  0.80 (0.21), residues: 602
  sheet: -1.74 (0.48), residues: 106
  loop : -1.67 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 340 
 TYR   0.019   0.001   TYR A 769 
 PHE   0.009   0.001   PHE A 780 
 TRP   0.005   0.001   TRP B 579 
 HIS   0.017   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.17 ( 8716)
  covalent geometry    : angle       0.63575 /  0.33 (11773)
  hydrogen bonds       : bond        0.04436 /  2.92 (  477)
  hydrogen bonds       : angle       4.88003 /  3.39 ( 1404)
  Misc. bond           : bond        0.00201 /  0.10 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 197
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7729 (t0) cc_final: 0.7237 (t0)
REVERT: A  344 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7449 (tm-30)
REVERT: A  369 ASP cc_start: 0.5909 (OUTLIER) cc_final: 0.5699 (m-30)
REVERT: A  562 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7389 (mp0)
REVERT: A  584 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6986 (tp)
REVERT: A  592 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8093 (ptt)
REVERT: A  629 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7067 (mp10)
REVERT: A  691 ILE cc_start: 0.7953 (mt) cc_final: 0.7621 (mt)
REVERT: A  778 CYS cc_start: 0.8097 (t) cc_final: 0.7888 (t)
REVERT: B  688 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7135 (mp)
REVERT: B  839 LYS cc_start: 0.8326 (tppp) cc_final: 0.8049 (tttm)
REVERT: B  889 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7237 (mt-10)
REVERT: B  917 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8388 (mt0)
REVERT: B  994 LEU cc_start: 0.6407 (tp) cc_final: 0.5560 (tp)
REVERT: B 1084 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7685 (mtpp)
  outliers start: 62
  outliers final: 48
  residues processed: 236
  average time/residue: 0.1058
  time to fit residues: 33.3666
Evaluate side-chains
  250 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 195
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  728 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue  561 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  688 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue  931 ILE
Chi-restraints excluded: chain B residue 1005 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 2 optimal weight:    0.0050
   chunk 1 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0770
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   overall best weight:    0.2330

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 GLN
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.161814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.143570 restraints weight = 12547.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4009 rms_B_bonded: 2.08
r_work: 0.3914 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3770 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8718  Z= 0.130
  Angle     :  0.618  11.264  11773  Z= 0.319
  Chirality :  0.044   0.277   1353
  Planarity :  0.004   0.045   1489
  Dihedral  : 10.795 167.993   1225
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 28.87 %
    Favored  : 65.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.26), residues: 1049
  helix:  0.95 (0.21), residues: 602
  sheet: -1.74 (0.49), residues: 100
  loop : -1.67 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 389 
 TYR   0.012   0.001   TYR B 629 
 PHE   0.009   0.001   PHE B 652 
 TRP   0.007   0.001   TRP B 807 
 HIS   0.017   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 8716)
  covalent geometry    : angle       0.61764 /  0.32 (11773)
  hydrogen bonds       : bond        0.04210 /  2.78 (  477)
  hydrogen bonds       : angle       4.83401 /  3.36 ( 1404)
  Misc. bond           : bond        0.00122 /  0.06 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 200
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7490 (t0) cc_final: 0.7001 (t0)
REVERT: A  344 GLN cc_start: 0.7778 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: A  584 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6949 (tp)
REVERT: A  592 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8053 (ptt)
REVERT: A  629 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7016 (mp10)
REVERT: B  688 ILE cc_start: 0.7535 (mp) cc_final: 0.7107 (mp)
REVERT: B  839 LYS cc_start: 0.8270 (tppp) cc_final: 0.7984 (tttm)
REVERT: B  917 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8366 (mt0)
REVERT: B  975 ASP cc_start: 0.7673 (t70) cc_final: 0.7274 (t0)
REVERT: B  994 LEU cc_start: 0.6166 (tp) cc_final: 0.5315 (tp)
REVERT: B 1084 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7680 (mtpp)
  outliers start: 53
  outliers final: 42
  residues processed: 233
  average time/residue: 0.1056
  time to fit residues: 32.7746
Evaluate side-chains
  242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 196
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  728 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain B residue  568 LYS
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  711 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1005 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Chi-restraints excluded: chain B residue 1097 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0770
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0020
   chunk 91 optimal weight:    0.4980
   overall best weight:    0.4946

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 544 ASN
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.160661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.142400 restraints weight = 12569.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 2.08
r_work: 0.3893 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8718  Z= 0.163
  Angle     :  0.659  11.680  11773  Z= 0.340
  Chirality :  0.045   0.290   1353
  Planarity :  0.005   0.046   1489
  Dihedral  : 10.805 168.668   1223
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 15.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 30.04 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.36 (0.26), residues: 1049
  helix:  0.84 (0.21), residues: 607
  sheet: -1.72 (0.49), residues: 100
  loop : -1.66 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 389 
 TYR   0.017   0.001   TYR A 769 
 PHE   0.008   0.001   PHE B 652 
 TRP   0.017   0.002   TRP A 345 
 HIS   0.021   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 8716)
  covalent geometry    : angle       0.65941 /  0.34 (11773)
  hydrogen bonds       : bond        0.04320 /  2.85 (  477)
  hydrogen bonds       : angle       4.86752 /  3.38 ( 1404)
  Misc. bond           : bond        0.00197 /  0.09 (    2)

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

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

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2098 Ramachandran restraints generated.
    1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 191
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 ASN cc_start: 0.7691 (t0) cc_final: 0.7197 (t0)
REVERT: A  344 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7416 (tm-30)
REVERT: A  345 TRP cc_start: 0.7604 (m-10) cc_final: 0.7278 (m-10)
REVERT: A  464 GLU cc_start: 0.7618 (pm20) cc_final: 0.7393 (mp0)
REVERT: A  562 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7531 (mp0)
REVERT: A  584 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6966 (tp)
REVERT: A  592 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8083 (ptt)
REVERT: A  629 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7057 (mp10)
REVERT: B  688 ILE cc_start: 0.7615 (mp) cc_final: 0.7167 (mp)
REVERT: B  839 LYS cc_start: 0.8315 (tppp) cc_final: 0.8081 (tttm)
REVERT: B  917 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8395 (mt0)
REVERT: B  975 ASP cc_start: 0.7798 (t70) cc_final: 0.7236 (t0)
REVERT: B  994 LEU cc_start: 0.6227 (tp) cc_final: 0.5377 (tp)
REVERT: B 1084 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7661 (mtpp)
  outliers start: 51
  outliers final: 40
  residues processed: 221
  average time/residue: 0.0948
  time to fit residues: 27.6579
Evaluate side-chains
  234 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 189
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  351 MET
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  404 CYS
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  584 ILE
Chi-restraints excluded: chain A residue  592 MET
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  629 GLN
Chi-restraints excluded: chain A residue  681 GLN
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  728 GLU
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  641 ILE
Chi-restraints excluded: chain B residue  656 ILE
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain B residue  675 ILE
Chi-restraints excluded: chain B residue  689 LEU
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  731 GLN
Chi-restraints excluded: chain B residue  753 MET
Chi-restraints excluded: chain B residue  788 ASN
Chi-restraints excluded: chain B residue  808 LEU
Chi-restraints excluded: chain B residue  822 CYS
Chi-restraints excluded: chain B residue  850 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  890 ARG
Chi-restraints excluded: chain B residue  895 THR
Chi-restraints excluded: chain B residue  913 THR
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue 1005 THR
Chi-restraints excluded: chain B residue 1033 LEU
Chi-restraints excluded: chain B residue 1059 ILE
Chi-restraints excluded: chain B residue 1066 ARG
Chi-restraints excluded: chain B residue 1097 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0050
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0170
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.4032

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 731 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.161097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.143042 restraints weight = 12587.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 2.08
r_work: 0.3900 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8718  Z= 0.152
  Angle     :  0.653  11.525  11773  Z= 0.340
  Chirality :  0.045   0.266   1353
  Planarity :  0.004   0.047   1489
  Dihedral  : 10.814 171.086   1223
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 29.83 %
    Favored  : 64.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.26), residues: 1049
  helix:  0.82 (0.21), residues: 607
  sheet: -1.70 (0.48), residues: 106
  loop : -1.67 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 389 
 TYR   0.014   0.001   TYR A 769 
 PHE   0.009   0.001   PHE A 780 
 TRP   0.015   0.002   TRP B 807 
 HIS   0.024   0.001   HIS B 729 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 8716)
  covalent geometry    : angle       0.65263 /  0.34 (11773)
  hydrogen bonds       : bond        0.04323 /  2.87 (  477)
  hydrogen bonds       : angle       4.86714 /  3.38 ( 1404)
  Misc. bond           : bond        0.00179 /  0.09 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2680.98 seconds
wall clock time: 46 minutes 39.55 seconds (2799.55 seconds total)