Starting phenix.real_space_refine
on Wed Aug  5 16:19:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uzb_42838/08_2026/8uzb_42838.map"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     162      5.49       5
     S      19      5.16       5
     C    6286      2.51       5
     N    1973      2.21       5
     O    2442      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10882
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 910, 7485
          Classifications: {'peptide': 910}
          Link IDs: {'PTRANS': 39, 'TRANS': 870}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 2267
          Classifications: {'RNA': 107}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53}
          Link IDs: {'rna2p': 9, 'rna3p': 97}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 808
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
    Chain: "D"
      Number of atoms: 322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 322
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 2.21, per 1000 atoms: 0.20
  Number of scatterers: 10882
  At special positions: 0
  Unit cell: (97.65, 123.69, 132.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     162     15.00
     O    2442      8.00
     N    1973      7.00
     C    6286      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 369.5 milliseconds
  

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      45.1% alpha, 14.5% beta
      68 base pairs and 109 stacking pairs defined.
    Time for finding SS restraints: 1.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 78
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 4.539A  pdb=" N   PHE A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 110 through 124
      removed outlier: 3.777A  pdb=" N   ARG A 124 " --> pdb=" O   HIS A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 155
      removed outlier: 3.699A  pdb=" N   SER A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 168 through 171
    Processing helix  chain 'A' and resid 186 through 205
    Processing helix  chain 'A' and resid 210 through 222
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 253 through 268
    Processing helix  chain 'A' and resid 280 through 294
    Processing helix  chain 'A' and resid 299 through 306
    Processing helix  chain 'A' and resid 324 through 329
    Processing helix  chain 'A' and resid 336 through 351
    Processing helix  chain 'A' and resid 353 through 358
      removed outlier: 4.184A  pdb=" N   SER A 356 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 373
      removed outlier: 3.534A  pdb=" N   PHE A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 383
    Processing helix  chain 'A' and resid 403 through 411
    Processing helix  chain 'A' and resid 422 through 434
      Proline residue:  A 431  - end of helix
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 470 through 492
    Processing helix  chain 'A' and resid 503 through 506
      removed outlier: 4.097A  pdb=" N   SER A 506 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 503 through 506'
    Processing helix  chain 'A' and resid 508 through 523
    Processing helix  chain 'A' and resid 667 through 679
    Processing helix  chain 'A' and resid 696 through 707
      removed outlier: 3.816A  pdb=" N   THR A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   HIS A 702 " --> pdb=" O   ARG A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 729
      removed outlier: 3.673A  pdb=" N   VAL A 722 " --> pdb=" O   LEU A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 748
      removed outlier: 3.610A  pdb=" N   ILE A 735 " --> pdb=" O   THR A 731 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ALA A 736 " --> pdb=" O   PRO A 732 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS A 737 " --> pdb=" O   SER A 733 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 738 " --> pdb=" O   ASP A 734 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG A 744 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 746 " --> pdb=" O   TYR A 742 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLN A 747 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 774
      removed outlier: 4.557A  pdb=" N   ARG A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 777 through 785
      removed outlier: 3.502A  pdb=" N   LEU A 785 " --> pdb=" O   SER A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 796
    Processing helix  chain 'A' and resid 842 through 844
      No H-bonds generated for 'chain 'A' and resid 842 through 844'
    Processing helix  chain 'A' and resid 860 through 874
      removed outlier: 3.565A  pdb=" N   TYR A 864 " --> pdb=" O   ASP A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 882
    Processing helix  chain 'A' and resid 945 through 951
    Processing helix  chain 'A' and resid 963 through 967
    Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694
      removed outlier: 6.286A  pdb=" N   ILE A 497 " --> pdb=" O   TYR A 693 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   VAL A  14 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   VAL A  31 " --> pdb=" O   VAL A  14 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TRP A  16 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   LEU A  29 " --> pdb=" O   TRP A  16 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   VAL A  18 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298
      removed outlier: 6.784A  pdb=" N   ILE A 297 " --> pdb=" O   PHE A 333 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 388
      removed outlier: 4.110A  pdb=" N   TYR A 387 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 826
      removed outlier: 5.818A  pdb=" N   TYR A 823 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   VAL A 836 " --> pdb=" O   TYR A 823 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 887 through 889
    Processing sheet with id=AA7, first strand: chain 'A' and resid 911 through 914
      removed outlier: 4.370A  pdb=" N   THR A 919 " --> pdb=" O   LEU A 914 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 937 through 944
      removed outlier: 6.394A  pdb=" N   VAL A 929 " --> pdb=" O   SER A 979 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   SER A 979 " --> pdb=" O   VAL A 929 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   VAL A 931 " --> pdb=" O   ARG A 977 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 957
      removed outlier: 3.843A  pdb=" N   LYS A 968 " --> pdb=" O   ALA A 957 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1033 through 1038
      removed outlier: 5.318A  pdb=" N   LEU A1023 " --> pdb=" O   GLY A1036 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   THR A1015 " --> pdb=" O   GLU A1024 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ILE A1026 " --> pdb=" O   TYR A1013 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   TYR A1013 " --> pdb=" O   ILE A1026 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ASP A1008 " --> pdb=" O   ARG A 992 " (cutoff:3.500A)
      removed outlier: 11.580A  pdb=" N   ARG A 992 " --> pdb=" O   ASP A1008 " (cutoff:3.500A)
      removed outlier: 11.729A  pdb=" N   PHE A1010 " --> pdb=" O   LEU A 990 " (cutoff:3.500A)
      removed outlier: 11.298A  pdb=" N   LEU A 990 " --> pdb=" O   PHE A1010 " (cutoff:3.500A)
      removed outlier: 9.940A  pdb=" N   TYR A1012 " --> pdb=" O   ILE A 988 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   ILE A 988 " --> pdb=" O   TYR A1012 " (cutoff:3.500A)
      removed outlier: 9.883A  pdb=" N   LYS A1014 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   ILE A 986 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
      removed outlier: 11.110A  pdb=" N   ILE A1016 " --> pdb=" O   ASP A 984 " (cutoff:3.500A)
      removed outlier: 13.412A  pdb=" N   ASP A 984 " --> pdb=" O   ILE A1016 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LEU A 985 " --> pdb=" O   TYR A1048 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG A1044 " --> pdb=" O   GLU A 989 " (cutoff:3.500A)

    309 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      171 hydrogen bonds
      326 hydrogen bond angles
      0 basepair planarities
      68 basepair parallelities
      109 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2908
        1.34 -     1.46: 2984
        1.46 -     1.58: 5187
        1.58 -     1.70: 319
        1.70 -     1.82: 33
  Bond restraints: 11431
  Sorted by residual:
  bond pdb=" C3'  DC D  40 "
       pdb=" C2'  DC D  40 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.09e+01
  bond pdb=" C3'  DT C   6 "
       pdb=" C2'  DT C   6 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.39e+00
  bond pdb=" C3'  DA C  22 "
       pdb=" C2'  DA C  22 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.98e+00
  bond pdb=" C3'  DC C  24 "
       pdb=" C2'  DC C  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.34e+00
  bond pdb=" C3'  DG C  16 "
       pdb=" C2'  DG C  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.537 -0.021 8.00e-03 1.56e+04 6.86e+00
  ... (remaining 11426 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 15328
        1.46 -     2.92: 751
        2.92 -     4.39: 58
        4.39 -     5.85: 8
        5.85 -     7.31: 5
  Bond angle restraints: 16150
  Sorted by residual:
  angle pdb=" C3'   C B  77 "
        pdb=" O3'   C B  77 "
        pdb=" P     A B  78 "
      ideal   model   delta    sigma   weight residual
     119.70  124.88   -5.18 1.20e+00 6.94e-01 1.87e+01
  angle pdb=" N3   DT C  15 "
        pdb=" C4   DT C  15 "
        pdb=" O4   DT C  15 "
      ideal   model   delta    sigma   weight residual
     119.90  122.41   -2.51 6.00e-01 2.78e+00 1.75e+01
  angle pdb=" N3   DT C  30 "
        pdb=" C4   DT C  30 "
        pdb=" O4   DT C  30 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.73e+01
  angle pdb=" N3   DT D  31 "
        pdb=" C4   DT D  31 "
        pdb=" O4   DT D  31 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.70e+01
  angle pdb=" O4'  DA D  43 "
        pdb=" C4'  DA D  43 "
        pdb=" C3'  DA D  43 "
      ideal   model   delta    sigma   weight residual
     106.00  103.55    2.45 6.00e-01 2.78e+00 1.67e+01
  ... (remaining 16145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.01: 6437
       33.01 -    66.02: 539
       66.02 -    99.03: 41
       99.03 -   132.04: 0
      132.04 -   165.05: 3
  Dihedral angle restraints: 7020
    sinusoidal: 4348
      harmonic: 2672
  Sorted by residual:
  dihedral pdb=" C4'  DT C   6 "
           pdb=" C3'  DT C   6 "
           pdb=" O3'  DT C   6 "
           pdb=" P    DG C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.95  165.05     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'   C B  77 "
           pdb=" C3'   C B  77 "
           pdb=" O3'   C B  77 "
           pdb=" P     A B  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   55.03 -165.03     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DG C  16 "
           pdb=" C3'  DG C  16 "
           pdb=" O3'  DG C  16 "
           pdb=" P    DG C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.09  158.91     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 7017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1250
       0.038 -    0.075: 359
       0.075 -    0.113: 121
       0.113 -    0.150: 120
       0.150 -    0.188: 4
  Chirality restraints: 1854
  Sorted by residual:
  chirality pdb=" C3'   C B  77 "
            pdb=" C4'   C B  77 "
            pdb=" O3'   C B  77 "
            pdb=" C2'   C B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.56   -0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CB  THR A 416 "
            pdb=" CA  THR A 416 "
            pdb=" OG1 THR A 416 "
            pdb=" CG2 THR A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality pdb=" CA  TRP A 763 "
            pdb=" N   TRP A 763 "
            pdb=" C   TRP A 763 "
            pdb=" CB  TRP A 763 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.99e-01
  ... (remaining 1851 not shown)

  Planarity restraints: 1494
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 777 "   -0.041 5.00e-02 4.00e+02   6.19e-02 6.12e+00
        pdb=" N   PRO A 778 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 778 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 778 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  13 "    0.024 2.00e-02 2.50e+03   1.18e-02 3.50e+00
        pdb=" N1   DT C  13 "   -0.027 2.00e-02 2.50e+03
        pdb=" C2   DT C  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT C  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT C  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT C  13 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT C  13 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DT C  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT C  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DT C  13 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  93 "   -0.020 2.00e-02 2.50e+03   8.95e-03 2.40e+00
        pdb=" N9    G B  93 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    G B  93 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  93 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G B  93 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G B  93 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  93 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  93 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  93 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1491 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 396
        2.70 -     3.25: 9681
        3.25 -     3.80: 19056
        3.80 -     4.35: 25439
        4.35 -     4.90: 37296
  Nonbonded interactions: 91868
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 381 "
            pdb=" O   GLU A 386 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OG1 THR A  12 "
            pdb=" O   PHE A  34 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASP A 768 "
            pdb=" NH2 ARG A 771 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OD1 ASP A 337 "
            pdb=" NE2 GLN A 341 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OD2 ASP A  28 "
            pdb=" OH  TYR A 491 "
     model   vdw
     2.254 3.040
  ... (remaining 91863 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.720
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  11431  Z= 0.292
  Angle     :  0.662   7.309  16150  Z= 0.517
  Chirality :  0.051   0.188   1854
  Planarity :  0.004   0.062   1494
  Dihedral  : 20.256 165.051   5292
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.49 (0.28), residues: 902
  helix:  1.28 (0.27), residues: 375
  sheet: -0.76 (0.47), residues: 120
  loop : -0.12 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 503 
 TYR   0.020   0.001   TYR A 864 
 PHE   0.009   0.001   PHE A 759 
 TRP   0.013   0.001   TRP A 763 
 HIS   0.002   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.29 (11431)
  covalent geometry    : angle       0.66176 /  0.52 (16150)
  hydrogen bonds       : bond        0.15725 / 10.57 (  480)
  hydrogen bonds       : angle       5.45626 /  4.09 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.313 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.7702
  time to fit residues: 87.4169
Evaluate side-chains
  81 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.3586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.164796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.115348 restraints weight = 11138.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.52
r_work: 0.3141 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.0973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11431  Z= 0.213
  Angle     :  0.612   6.997  16150  Z= 0.345
  Chirality :  0.045   0.342   1854
  Planarity :  0.005   0.047   1494
  Dihedral  : 22.242 170.705   3337
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  9.37 %
    Favored  : 88.53 %
  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:  0.45 (0.28), residues: 902
  helix:  1.28 (0.27), residues: 387
  sheet: -0.77 (0.45), residues: 125
  loop : -0.22 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 698 
 TYR   0.022   0.002   TYR A 491 
 PHE   0.015   0.002   PHE A 932 
 TRP   0.009   0.001   TRP A 763 
 HIS   0.006   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00466 /  0.21 (11431)
  covalent geometry    : angle       0.61236 /  0.34 (16150)
  hydrogen bonds       : bond        0.06217 /  4.15 (  480)
  hydrogen bonds       : angle       4.19546 /  3.06 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8393 (m-30) cc_final: 0.7927 (m-30)
REVERT: A   92 LYS cc_start: 0.8276 (ptmt) cc_final: 0.7972 (ptmt)
REVERT: A  335 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7487 (mt-10)
REVERT: A  437 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (mt-10)
REVERT: A  460 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8212 (ttt)
REVERT: A  500 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7880 (tt0)
REVERT: A  696 ASN cc_start: 0.7986 (t0) cc_final: 0.7709 (t0)
  outliers start: 17
  outliers final: 3
  residues processed: 96
  average time/residue: 0.7306
  time to fit residues: 74.5978
Evaluate side-chains
  87 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  437 GLU
Chi-restraints excluded: chain A residue  460 MET
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  795 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 23 optimal weight:    0.1980
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.1986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.166592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.115109 restraints weight = 11241.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.60
r_work: 0.3190 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11431  Z= 0.146
  Angle     :  0.529   6.841  16150  Z= 0.305
  Chirality :  0.041   0.343   1854
  Planarity :  0.004   0.033   1494
  Dihedral  : 22.244 169.582   3337
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 11.10 %
    Favored  : 86.81 %
  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:  0.61 (0.28), residues: 902
  helix:  1.50 (0.27), residues: 387
  sheet: -1.12 (0.44), residues: 122
  loop : -0.07 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 393 
 TYR   0.012   0.001   TYR A 491 
 PHE   0.010   0.001   PHE A 932 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.15 (11431)
  covalent geometry    : angle       0.52938 /  0.31 (16150)
  hydrogen bonds       : bond        0.05406 /  3.61 (  480)
  hydrogen bonds       : angle       4.00061 /  2.92 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8379 (m-30) cc_final: 0.7878 (m-30)
REVERT: A  335 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7474 (mt-10)
REVERT: A  337 ASP cc_start: 0.8221 (t70) cc_final: 0.7822 (t0)
REVERT: A  457 GLN cc_start: 0.7578 (tp40) cc_final: 0.7354 (tp-100)
REVERT: A  696 ASN cc_start: 0.7986 (t0) cc_final: 0.7692 (t0)
REVERT: A  869 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7407 (mm-40)
REVERT: A 1044 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7735 (ttm-80)
  outliers start: 17
  outliers final: 7
  residues processed: 100
  average time/residue: 0.7398
  time to fit residues: 78.7653
Evaluate side-chains
  89 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 94 optimal weight:   20.0000
   chunk 76 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   overall best weight:    1.4782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.165736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114158 restraints weight = 11266.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.60
r_work: 0.3183 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11431  Z= 0.156
  Angle     :  0.539   6.927  16150  Z= 0.307
  Chirality :  0.041   0.342   1854
  Planarity :  0.004   0.042   1494
  Dihedral  : 22.235 169.630   3337
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.10 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.28), residues: 902
  helix:  1.55 (0.27), residues: 387
  sheet: -1.00 (0.45), residues: 115
  loop : -0.11 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1060 
 TYR   0.012   0.001   TYR A 864 
 PHE   0.012   0.001   PHE A 932 
 TRP   0.008   0.001   TRP A 763 
 HIS   0.005   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (11431)
  covalent geometry    : angle       0.53935 /  0.31 (16150)
  hydrogen bonds       : bond        0.05297 /  3.53 (  480)
  hydrogen bonds       : angle       3.89717 /  2.85 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8375 (m-30) cc_final: 0.7842 (m-30)
REVERT: A  335 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7560 (mt-10)
REVERT: A  337 ASP cc_start: 0.8182 (t70) cc_final: 0.7774 (t0)
REVERT: A  457 GLN cc_start: 0.7622 (tp40) cc_final: 0.7389 (tp-100)
REVERT: A  500 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7894 (tt0)
REVERT: A  696 ASN cc_start: 0.8130 (t0) cc_final: 0.7777 (t0)
REVERT: A  798 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (mp)
REVERT: A  869 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7419 (mm-40)
REVERT: A  948 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8214 (mt)
REVERT: A 1044 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7700 (ttm-80)
  outliers start: 19
  outliers final: 7
  residues processed: 96
  average time/residue: 0.7002
  time to fit residues: 71.6110
Evaluate side-chains
  91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0170
   chunk 89 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.0420

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 290 GLN
A 793 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.166679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.115300 restraints weight = 11214.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.59
r_work: 0.3194 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11431  Z= 0.134
  Angle     :  0.522   6.956  16150  Z= 0.299
  Chirality :  0.040   0.341   1854
  Planarity :  0.004   0.033   1494
  Dihedral  : 22.235 169.637   3337
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.22 %
    Favored  : 86.31 %
  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:  0.78 (0.28), residues: 902
  helix:  1.67 (0.27), residues: 385
  sheet: -0.99 (0.46), residues: 115
  loop : -0.06 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1060 
 TYR   0.012   0.001   TYR A 864 
 PHE   0.010   0.001   PHE A 932 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 (11431)
  covalent geometry    : angle       0.52233 /  0.30 (16150)
  hydrogen bonds       : bond        0.05054 /  3.38 (  480)
  hydrogen bonds       : angle       3.80962 /  2.78 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   28 ASP cc_start: 0.8383 (m-30) cc_final: 0.7791 (m-30)
REVERT: A  337 ASP cc_start: 0.8135 (t70) cc_final: 0.7771 (t0)
REVERT: A  457 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7411 (tp-100)
REVERT: A  500 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7903 (tt0)
REVERT: A  696 ASN cc_start: 0.8192 (t0) cc_final: 0.7851 (t0)
REVERT: A  798 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7003 (mp)
REVERT: A  817 ARG cc_start: 0.8892 (mmp-170) cc_final: 0.8661 (mmm160)
REVERT: A  869 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7439 (mm-40)
REVERT: A  966 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7608 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7700 (ttm-80)
  outliers start: 20
  outliers final: 7
  residues processed: 98
  average time/residue: 0.6202
  time to fit residues: 64.6662
Evaluate side-chains
  95 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 102 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9990
   overall best weight:    3.0188

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.163082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120462 restraints weight = 11224.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.17
r_work: 0.3083 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  11431  Z= 0.244
  Angle     :  0.632   7.975  16150  Z= 0.349
  Chirality :  0.047   0.338   1854
  Planarity :  0.006   0.051   1494
  Dihedral  : 22.309 170.572   3337
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.21 %
    Favored  : 84.96 %
  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:  0.43 (0.28), residues: 902
  helix:  1.41 (0.27), residues: 381
  sheet: -1.04 (0.44), residues: 120
  loop : -0.30 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1060 
 TYR   0.015   0.002   TYR A 864 
 PHE   0.018   0.002   PHE A 932 
 TRP   0.008   0.001   TRP A 763 
 HIS   0.010   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.24 (11431)
  covalent geometry    : angle       0.63249 /  0.35 (16150)
  hydrogen bonds       : bond        0.06049 /  4.06 (  480)
  hydrogen bonds       : angle       3.90761 /  2.85 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  335 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7509 (mt-10)
REVERT: A  337 ASP cc_start: 0.8192 (t70) cc_final: 0.7786 (t0)
REVERT: A  457 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7523 (tp-100)
REVERT: A  500 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8032 (tt0)
REVERT: A  798 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7038 (mp)
REVERT: A  869 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7467 (mm-40)
REVERT: A  948 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (mt)
REVERT: A  966 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7648 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7728 (ttm-80)
  outliers start: 23
  outliers final: 9
  residues processed: 97
  average time/residue: 0.7067
  time to fit residues: 72.8652
Evaluate side-chains
  92 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1003 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 5 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 96 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 793 GLN
A1005 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.165907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.123814 restraints weight = 11227.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.17
r_work: 0.3124 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11431  Z= 0.146
  Angle     :  0.545   7.012  16150  Z= 0.310
  Chirality :  0.041   0.339   1854
  Planarity :  0.004   0.032   1494
  Dihedral  : 22.285 170.562   3337
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.32 %
    Favored  : 83.97 %
  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:  0.59 (0.28), residues: 902
  helix:  1.54 (0.27), residues: 387
  sheet: -1.07 (0.45), residues: 115
  loop : -0.19 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1060 
 TYR   0.013   0.001   TYR A 864 
 PHE   0.011   0.001   PHE A 932 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.15 (11431)
  covalent geometry    : angle       0.54512 /  0.31 (16150)
  hydrogen bonds       : bond        0.05244 /  3.52 (  480)
  hydrogen bonds       : angle       3.81042 /  2.78 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   38 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7910 (pm20)
REVERT: A   81 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8022 (p)
REVERT: A  290 GLN cc_start: 0.6978 (tt0) cc_final: 0.5947 (mp10)
REVERT: A  335 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7567 (mt-10)
REVERT: A  337 ASP cc_start: 0.8155 (t70) cc_final: 0.7751 (t0)
REVERT: A  500 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8033 (tt0)
REVERT: A  798 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7030 (mp)
REVERT: A  869 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7496 (mm-40)
REVERT: A  966 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7681 (mt-10)
REVERT: A 1044 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7685 (ttm-80)
  outliers start: 22
  outliers final: 9
  residues processed: 102
  average time/residue: 0.6808
  time to fit residues: 73.4326
Evaluate side-chains
  97 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   38 GLU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  966 GLU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 100 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9980
   chunk 85 optimal weight:    0.1980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.132613 restraints weight = 11228.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.05
r_work: 0.3223 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  11431  Z= 0.119
  Angle     :  0.513   6.966  16150  Z= 0.294
  Chirality :  0.039   0.341   1854
  Planarity :  0.004   0.051   1494
  Dihedral  : 22.243 169.539   3337
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.29 %
    Favored  : 82.74 %
  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:  0.79 (0.28), residues: 902
  helix:  1.70 (0.27), residues: 387
  sheet: -1.09 (0.45), residues: 122
  loop : -0.03 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1060 
 TYR   0.013   0.001   TYR A 864 
 PHE   0.009   0.001   PHE A 932 
 TRP   0.009   0.001   TRP A 763 
 HIS   0.003   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 (11431)
  covalent geometry    : angle       0.51294 /  0.29 (16150)
  hydrogen bonds       : bond        0.04766 /  3.19 (  480)
  hydrogen bonds       : angle       3.68066 /  2.67 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   81 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8256 (p)
REVERT: A  337 ASP cc_start: 0.8189 (t70) cc_final: 0.7865 (t0)
REVERT: A  500 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8087 (tt0)
REVERT: A  798 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7371 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 101
  average time/residue: 0.6437
  time to fit residues: 68.9828
Evaluate side-chains
  93 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   chunk 97 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 GLN
A 793 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.169107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.129941 restraints weight = 11169.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.05
r_work: 0.3188 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11431  Z= 0.160
  Angle     :  0.549   7.087  16150  Z= 0.308
  Chirality :  0.042   0.340   1854
  Planarity :  0.004   0.036   1494
  Dihedral  : 22.230 169.853   3337
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.03 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.28), residues: 902
  helix:  1.65 (0.27), residues: 387
  sheet: -0.90 (0.46), residues: 115
  loop : -0.10 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1031 
 TYR   0.018   0.001   TYR A 864 
 PHE   0.011   0.001   PHE A 932 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.005   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.16 (11431)
  covalent geometry    : angle       0.54883 /  0.31 (16150)
  hydrogen bonds       : bond        0.05077 /  3.40 (  480)
  hydrogen bonds       : angle       3.70543 /  2.69 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A  306 LEU cc_start: 0.7520 (mp) cc_final: 0.6859 (pp)
REVERT: A  335 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7665 (mt-10)
REVERT: A  337 ASP cc_start: 0.8205 (t70) cc_final: 0.7871 (t0)
REVERT: A  500 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8109 (tt0)
REVERT: A  798 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7405 (mp)
REVERT: A 1044 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7947 (ttm-80)
  outliers start: 16
  outliers final: 8
  residues processed: 94
  average time/residue: 0.7170
  time to fit residues: 71.6398
Evaluate side-chains
  94 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  500 GLU
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue 1044 ARG
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0060
   chunk 21 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.6998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.170404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.131697 restraints weight = 11178.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.02
r_work: 0.3214 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  11431  Z= 0.123
  Angle     :  0.534   8.877  16150  Z= 0.303
  Chirality :  0.040   0.340   1854
  Planarity :  0.004   0.041   1494
  Dihedral  : 22.239 169.870   3337
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 17.14 %
    Favored  : 81.26 %
  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:  0.86 (0.28), residues: 902
  helix:  1.75 (0.27), residues: 387
  sheet: -0.88 (0.46), residues: 115
  loop : -0.06 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1060 
 TYR   0.019   0.001   TYR A 864 
 PHE   0.007   0.001   PHE A 882 
 TRP   0.008   0.001   TRP A 763 
 HIS   0.005   0.001   HIS A 720 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 (11431)
  covalent geometry    : angle       0.53410 /  0.30 (16150)
  hydrogen bonds       : bond        0.04805 /  3.22 (  480)
  hydrogen bonds       : angle       3.69972 /  2.69 ( 1214)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  306 LEU cc_start: 0.7462 (mp) cc_final: 0.6887 (pp)
REVERT: A  335 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7654 (mt-10)
REVERT: A  337 ASP cc_start: 0.8189 (t70) cc_final: 0.7862 (t0)
REVERT: A  798 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: A  869 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7791 (mm-40)
  outliers start: 13
  outliers final: 8
  residues processed: 92
  average time/residue: 0.7995
  time to fit residues: 78.0030
Evaluate side-chains
  91 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain A residue  666 THR
Chi-restraints excluded: chain A residue  670 SER
Chi-restraints excluded: chain A residue  705 SER
Chi-restraints excluded: chain A residue  795 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue 1046 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 102 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.170035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.130809 restraints weight = 11169.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.07
r_work: 0.3200 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11431  Z= 0.137
  Angle     :  0.541   9.125  16150  Z= 0.304
  Chirality :  0.041   0.340   1854
  Planarity :  0.004   0.037   1494
  Dihedral  : 22.205 169.898   3337
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.65 %
    Favored  : 81.38 %
  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:  0.83 (0.28), residues: 902
  helix:  1.71 (0.27), residues: 387
  sheet: -0.89 (0.46), residues: 115
  loop : -0.06 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1031 
 TYR   0.021   0.001   TYR A 864 
 PHE   0.008   0.001   PHE A 932 
 TRP   0.007   0.001   TRP A 763 
 HIS   0.004   0.001   HIS A1028 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.14 (11431)
  covalent geometry    : angle       0.54111 /  0.30 (16150)
  hydrogen bonds       : bond        0.04892 /  3.28 (  480)
  hydrogen bonds       : angle       3.65955 /  2.66 ( 1214)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3910.98 seconds
wall clock time: 67 minutes 10.42 seconds (4030.42 seconds total)