Starting phenix.real_space_refine
on Fri Jul  3 04:31:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rbo_53900/07_2026/9rbo_53900.map"
  }
  resolution = 3.0
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    7351      2.51       5
     N    1975      2.21       5
     O    2221      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 11606
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1553
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "B"
      Number of atoms: 2443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2443
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 19, 'TRANS': 296}
    Chain: "C"
      Number of atoms: 405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 405
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 2, 'TRANS': 46}
    Chain: "D"
      Number of atoms: 7205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 902, 7205
          Classifications: {'peptide': 902}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 40, 'TRANS': 861}
  Time building chain proxies: 2.69, per 1000 atoms: 0.23
  Number of scatterers: 11606
  At special positions: 0
  Unit cell: (123.768, 122.472, 138.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    2221      8.00
     N    1975      7.00
     C    7351      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 605 " - pdb=" SG  CYS B 640 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 671 " - pdb=" SG  CYS C 698 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 672 " - pdb=" SG  CYS C 705 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 685 " - pdb=" SG  CYS C 706 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 851 " - pdb=" SG  CYS D1491 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D1079 " - pdb=" SG  CYS D1136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D1336 " - pdb=" SG  CYS D1467 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D1367 " - pdb=" SG  CYS D1436 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D1484 " - pdb=" SG  CYS D1489 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D1496 " - pdb=" SG  CYS D1568 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D1515 " - pdb=" SG  CYS D1639 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D1615 " - pdb=" SG  CYS D1624 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 472.5 milliseconds
  

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2762

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      20.8% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'B' and resid 459 through 465
    Processing helix  chain 'B' and resid 574 through 578
      removed outlier: 3.709A  pdb=" N   LYS B 578 " --> pdb=" O   ALA B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 603
      removed outlier: 4.306A  pdb=" N   ILE B 603 " --> pdb=" O   LYS B 600 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 666 through 677
      removed outlier: 3.788A  pdb=" N   CYS C 672 " --> pdb=" O   LEU C 668 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 695 through 712
      removed outlier: 3.583A  pdb=" N   GLU C 711 " --> pdb=" O   ASN C 707 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU C 712 " --> pdb=" O   TYR C 708 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 966 through 974
    Processing helix  chain 'D' and resid 977 through 982
    Processing helix  chain 'D' and resid 990 through 995
    Processing helix  chain 'D' and resid 996 through 1008
    Processing helix  chain 'D' and resid 1011 through 1016
    Processing helix  chain 'D' and resid 1017 through 1035
      removed outlier: 3.625A  pdb=" N   GLN D1021 " --> pdb=" O   LEU D1017 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1036 through 1038
      No H-bonds generated for 'chain 'D' and resid 1036 through 1038'
    Processing helix  chain 'D' and resid 1053 through 1067
    Processing helix  chain 'D' and resid 1074 through 1088
      removed outlier: 3.760A  pdb=" N   LEU D1078 " --> pdb=" O   ASP D1074 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA D1081 " --> pdb=" O   VAL D1077 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1119 through 1132
    Processing helix  chain 'D' and resid 1142 through 1158
    Processing helix  chain 'D' and resid 1159 through 1161
      No H-bonds generated for 'chain 'D' and resid 1159 through 1161'
    Processing helix  chain 'D' and resid 1163 through 1178
      removed outlier: 3.740A  pdb=" N   MET D1177 " --> pdb=" O   ALA D1173 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1182 through 1192
      removed outlier: 3.846A  pdb=" N   ALA D1192 " --> pdb=" O   PHE D1188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1203 through 1221
    Processing helix  chain 'D' and resid 1226 through 1236
      removed outlier: 4.163A  pdb=" N   VAL D1230 " --> pdb=" O   PHE D1226 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1246 through 1263
      removed outlier: 3.593A  pdb=" N   GLN D1261 " --> pdb=" O   LEU D1257 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1392 through 1401
    Processing helix  chain 'D' and resid 1487 through 1494
      removed outlier: 3.579A  pdb=" N   GLU D1494 " --> pdb=" O   ARG D1490 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1506 through 1515
    Processing helix  chain 'D' and resid 1568 through 1573
    Processing helix  chain 'D' and resid 1587 through 1589
      No H-bonds generated for 'chain 'D' and resid 1587 through 1589'
    Processing helix  chain 'D' and resid 1611 through 1615
    Processing helix  chain 'D' and resid 1623 through 1637
      removed outlier: 3.551A  pdb=" N   GLY D1628 " --> pdb=" O   CYS D1624 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE D1637 " --> pdb=" O   SER D1633 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109
      removed outlier: 3.706A  pdb=" N   TYR A 107 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   VAL A 130 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   PHE A 109 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   PHE A 128 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144
      removed outlier: 3.649A  pdb=" N   TYR A 187 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 367 through 369
      removed outlier: 3.513A  pdb=" N   ALA B 368 " --> pdb=" O   ARG B 403 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 398 through 400
    Processing sheet with id=AA5, first strand: chain 'B' and resid 437 through 438
    Processing sheet with id=AA6, first strand: chain 'D' and resid 809 through 812
      removed outlier: 3.611A  pdb=" N   VAL D 874 " --> pdb=" O   ALA D 827 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 809 through 812
    Processing sheet with id=AA8, first strand: chain 'D' and resid 816 through 818
      removed outlier: 6.101A  pdb=" N   VAL D 817 " --> pdb=" O   VAL D 910 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 862 through 866
      removed outlier: 3.703A  pdb=" N   VAL D 903 " --> pdb=" O   VAL D 890 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 914 through 921
      removed outlier: 3.550A  pdb=" N   TYR D1326 " --> pdb=" O   MET D 916 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   VAL D1322 " --> pdb=" O   VAL D 920 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 937 through 940
      removed outlier: 3.508A  pdb=" N   ILE D1285 " --> pdb=" O   LEU D1276 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 1339 through 1347
    Processing sheet with id=AB4, first strand: chain 'D' and resid 1409 through 1410
      removed outlier: 3.605A  pdb=" N   LYS D1409 " --> pdb=" O   TYR D1425 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 1598 through 1599
      removed outlier: 3.686A  pdb=" N   LYS D1529 " --> pdb=" O   ILE D1540 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ALA D1542 " --> pdb=" O   LEU D1527 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   LEU D1527 " --> pdb=" O   ALA D1542 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   GLU D1544 " --> pdb=" O   THR D1525 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   THR D1525 " --> pdb=" O   GLU D1544 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   THR D1546 " --> pdb=" O   TYR D1523 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TYR D1523 " --> pdb=" O   THR D1546 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LYS D1548 " --> pdb=" O   TYR D1521 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TYR D1521 " --> pdb=" O   LYS D1548 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   GLY D1584 " --> pdb=" O   ASP D1520 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   VAL D1522 " --> pdb=" O   MET D1582 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   MET D1582 " --> pdb=" O   VAL D1522 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS D1524 " --> pdb=" O   TYR D1580 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR D1580 " --> pdb=" O   LYS D1524 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ARG D1526 " --> pdb=" O   LYS D1578 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LYS D1578 " --> pdb=" O   ARG D1526 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   HIS D1579 " --> pdb=" O   TRP D1609 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TRP D1583 " --> pdb=" O   TRP D1605 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    840 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3118
        1.33 -     1.46: 2946
        1.46 -     1.59: 5684
        1.59 -     1.72: 0
        1.72 -     1.84: 91
  Bond restraints: 11839
  Sorted by residual:
  bond pdb=" C   PHE A  40 "
       pdb=" N   PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.444 -0.109 8.70e-03 1.32e+04 1.58e+02
  bond pdb=" C   PRO A  41 "
       pdb=" N   GLY A  42 "
    ideal  model  delta    sigma   weight residual
    1.331  1.487 -0.157 1.46e-02 4.69e+03 1.15e+02
  bond pdb=" N   PRO A  41 "
       pdb=" CD  PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.473  1.559 -0.086 1.40e-02 5.10e+03 3.81e+01
  bond pdb=" N   GLU A  15 "
       pdb=" CA  GLU A  15 "
    ideal  model  delta    sigma   weight residual
    1.458  1.502 -0.044 1.08e-02 8.57e+03 1.64e+01
  bond pdb=" N   PHE A  40 "
       pdb=" CA  PHE A  40 "
    ideal  model  delta    sigma   weight residual
    1.462  1.499 -0.038 9.50e-03 1.11e+04 1.57e+01
  ... (remaining 11834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.79: 15872
        5.79 -    11.57: 148
       11.57 -    17.36: 12
       17.36 -    23.14: 6
       23.14 -    28.93: 3
  Bond angle restraints: 16041
  Sorted by residual:
  angle pdb=" N   ASP D1418 "
        pdb=" CA  ASP D1418 "
        pdb=" C   ASP D1418 "
      ideal   model   delta    sigma   weight residual
     112.04  140.50  -28.46 1.44e+00 4.82e-01 3.91e+02
  angle pdb=" N   ASN B 356 "
        pdb=" CA  ASN B 356 "
        pdb=" CB  ASN B 356 "
      ideal   model   delta    sigma   weight residual
     110.37   81.44   28.93 1.78e+00 3.16e-01 2.64e+02
  angle pdb=" N   SER B 506 "
        pdb=" CA  SER B 506 "
        pdb=" CB  SER B 506 "
      ideal   model   delta    sigma   weight residual
     110.86  129.96  -19.10 1.54e+00 4.22e-01 1.54e+02
  angle pdb=" N   LYS A 114 "
        pdb=" CA  LYS A 114 "
        pdb=" C   LYS A 114 "
      ideal   model   delta    sigma   weight residual
     108.74   92.57   16.17 1.38e+00 5.25e-01 1.37e+02
  angle pdb=" N   SER B 506 "
        pdb=" CA  SER B 506 "
        pdb=" C   SER B 506 "
      ideal   model   delta    sigma   weight residual
     107.20   87.78   19.42 1.70e+00 3.46e-01 1.31e+02
  ... (remaining 16036 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.99: 6459
       23.99 -    47.97: 652
       47.97 -    71.96: 123
       71.96 -    95.94: 26
       95.94 -   119.93: 1
  Dihedral angle restraints: 7261
    sinusoidal: 2989
      harmonic: 4272
  Sorted by residual:
  dihedral pdb=" CA  PRO D1040 "
           pdb=" C   PRO D1040 "
           pdb=" N   SER D1041 "
           pdb=" CA  SER D1041 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   60.07  119.93     0      5.00e+00 4.00e-02 5.75e+02
  dihedral pdb=" N   ASN B 356 "
           pdb=" C   ASN B 356 "
           pdb=" CA  ASN B 356 "
           pdb=" CB  ASN B 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   89.68   33.12     0      2.50e+00 1.60e-01 1.75e+02
  dihedral pdb=" CB  CYS B 605 "
           pdb=" SG  CYS B 605 "
           pdb=" SG  CYS B 640 "
           pdb=" CB  CYS B 640 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.07  -82.93     1      1.00e+01 1.00e-02 8.42e+01
  ... (remaining 7258 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.181: 1755
       0.181 -    0.362: 47
       0.362 -    0.542: 2
       0.542 -    0.723: 1
       0.723 -    0.904: 2
  Chirality restraints: 1807
  Sorted by residual:
  chirality pdb=" CA  PRO B 505 "
            pdb=" N   PRO B 505 "
            pdb=" C   PRO B 505 "
            pdb=" CB  PRO B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.81    0.90 2.00e-01 2.50e+01 2.04e+01
  chirality pdb=" CA  ASP D1418 "
            pdb=" N   ASP D1418 "
            pdb=" C   ASP D1418 "
            pdb=" CB  ASP D1418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.72    0.80 2.00e-01 2.50e+01 1.58e+01
  chirality pdb=" CA  ARG D1419 "
            pdb=" N   ARG D1419 "
            pdb=" C   ARG D1419 "
            pdb=" CB  ARG D1419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.10   -0.59 2.00e-01 2.50e+01 8.73e+00
  ... (remaining 1804 not shown)

  Planarity restraints: 2077
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 932 "    1.079 9.50e-02 1.11e+02   4.83e-01 1.41e+02
        pdb=" NE  ARG D 932 "   -0.065 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 932 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 932 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 932 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 570 "   -1.016 9.50e-02 1.11e+02   4.55e-01 1.25e+02
        pdb=" NE  ARG B 570 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 570 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 570 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 570 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 929 "   -0.946 9.50e-02 1.11e+02   4.24e-01 1.09e+02
        pdb=" NE  ARG D 929 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 929 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 929 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 929 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 2074 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 367
        2.66 -     3.22: 12568
        3.22 -     3.78: 19803
        3.78 -     4.34: 25979
        4.34 -     4.90: 40355
  Nonbonded interactions: 99072
  Sorted by model distance:
  nonbonded pdb=" O   HIS A  38 "
            pdb=" OD1 ASP A  39 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" N   LYS A 114 "
            pdb=" O   LYS A 114 "
     model   vdw
     2.208 2.496
  nonbonded pdb=" CD2 TYR B 331 "
            pdb=" OE1 GLN B 332 "
     model   vdw
     2.231 3.340
  nonbonded pdb=" O   GLU D1487 "
            pdb=" OE1 GLU D1487 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" OG  SER D 816 "
            pdb=" CG  LYS D 908 "
     model   vdw
     2.354 3.440
  ... (remaining 99067 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:             4.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.980
  Find NCS groups from input model:        0.060
  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:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
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      :  0.011   0.157  11851  Z= 0.529
  Angle     :  1.555  28.925  16065  Z= 0.857
  Chirality :  0.080   0.904   1807
  Planarity :  0.020   0.483   2077
  Dihedral  : 19.261 119.928   4463
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 40.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 15.05 %
    Favored  : 84.88 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 33.95 %
    Favored  : 62.19 %
  Cbeta Deviations :  0.80 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.20), residues: 1455
  helix: -0.41 (0.31), residues: 267
  sheet: -0.72 (0.32), residues: 274
  loop : -3.13 (0.18), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.002   ARG B 483 
 TYR   0.033   0.003   TYR B 468 
 PHE   0.075   0.004   PHE B 624 
 TRP   0.034   0.004   TRP A 171 
 HIS   0.007   0.002   HIS B 567 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01118 /  0.53 (11839)
  covalent geometry    : angle       1.55323 /  0.86 (16041)
  SS BOND              : bond        0.00978 /  0.71 (   12)
  SS BOND              : angle       2.32603 /  1.38 (   24)
  hydrogen bonds       : bond        0.14649 /  9.91 (  310)
  hydrogen bonds       : angle       7.24616 /  5.14 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 123
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 MET cc_start: 0.4876 (mmm) cc_final: 0.4599 (tpp)
REVERT: B  419 MET cc_start: 0.7654 (tmm) cc_final: 0.7196 (tmm)
REVERT: B  430 SER cc_start: 0.8910 (m) cc_final: 0.8599 (p)
REVERT: B  508 ARG cc_start: 0.5829 (tpt170) cc_final: 0.5515 (tpt-90)
REVERT: D 1181 LYS cc_start: 0.7858 (pttt) cc_final: 0.7580 (mmtm)
REVERT: D 1509 GLU cc_start: 0.9021 (pt0) cc_final: 0.8738 (pm20)
REVERT: D 1541 MET cc_start: 0.7200 (mmt) cc_final: 0.6386 (tpp)
REVERT: D 1545 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8362 (tm-30)
REVERT: D 1576 GLU cc_start: 0.7935 (pt0) cc_final: 0.7694 (pm20)
REVERT: D 1603 ASP cc_start: 0.8672 (m-30) cc_final: 0.7776 (t0)
  outliers start: 50
  outliers final: 28
  residues processed: 161
  average time/residue: 0.5425
  time to fit residues: 95.7935
Evaluate side-chains
  141 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  471 LEU
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  570 ARG
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  877 VAL
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1322 VAL
Chi-restraints excluded: chain D residue 1386 MET
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1418 ASP
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1501 SER
Chi-restraints excluded: chain D residue 1515 CYS
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1545 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 ASN
B 332 GLN
B 376 GLN
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN
D1114 ASN
** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.114403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.098230 restraints weight = 60237.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 6.07
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11851  Z= 0.159
  Angle     :  0.853  18.184  16065  Z= 0.429
  Chirality :  0.048   0.262   1807
  Planarity :  0.006   0.062   2077
  Dihedral  :  8.054  58.287   1630
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 21.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 14.16 %
    Favored  : 85.77 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 30.09 %
    Favored  : 63.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.21), residues: 1455
  helix: -0.25 (0.31), residues: 281
  sheet: -0.43 (0.33), residues: 253
  loop : -2.99 (0.18), residues: 921

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 508 
 TYR   0.017   0.002   TYR B 467 
 PHE   0.026   0.002   PHE B 617 
 TRP   0.017   0.002   TRP B 530 
 HIS   0.006   0.001   HIS A  25 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 (11839)
  covalent geometry    : angle       0.85192 /  0.43 (16041)
  SS BOND              : bond        0.00634 /  0.50 (   12)
  SS BOND              : angle       1.58810 /  0.93 (   24)
  hydrogen bonds       : bond        0.04003 /  2.73 (  310)
  hydrogen bonds       : angle       5.66032 /  4.00 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 126
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6809 (ttpp)
REVERT: A   61 MET cc_start: 0.7430 (mmt) cc_final: 0.6356 (mmt)
REVERT: B  419 MET cc_start: 0.7645 (tmm) cc_final: 0.7227 (tmm)
REVERT: B  457 MET cc_start: -0.0384 (OUTLIER) cc_final: -0.1760 (tmm)
REVERT: B  508 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5028 (ptp-170)
REVERT: D  804 MET cc_start: 0.6691 (tmm) cc_final: 0.6439 (tmm)
REVERT: D  899 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6138 (tt)
REVERT: D 1075 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7610 (t)
REVERT: D 1181 LYS cc_start: 0.7980 (pttt) cc_final: 0.7678 (mmtm)
REVERT: D 1379 SER cc_start: 0.6927 (OUTLIER) cc_final: 0.6711 (m)
REVERT: D 1541 MET cc_start: 0.6898 (mmt) cc_final: 0.6432 (tpp)
REVERT: D 1603 ASP cc_start: 0.8662 (m-30) cc_final: 0.7735 (t0)
  outliers start: 85
  outliers final: 30
  residues processed: 193
  average time/residue: 0.5003
  time to fit residues: 106.6955
Evaluate side-chains
  141 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 HIS
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  551 ARG
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain D residue  761 LYS
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  897 HIS
Chi-restraints excluded: chain D residue  899 ILE
Chi-restraints excluded: chain D residue  914 ILE
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1379 SER
Chi-restraints excluded: chain D residue 1386 MET
Chi-restraints excluded: chain D residue 1446 ASN
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1515 CYS
Chi-restraints excluded: chain D residue 1519 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   chunk 141 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 103 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN
D 917 ASN
** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.111924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.095602 restraints weight = 61309.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.4197 rms_B_bonded: 6.09
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11851  Z= 0.197
  Angle     :  0.834  15.464  16065  Z= 0.420
  Chirality :  0.048   0.256   1807
  Planarity :  0.005   0.061   2077
  Dihedral  :  7.459  58.513   1599
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 22.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 14.30 %
    Favored  : 85.57 %
  Rotamer:
    Outliers :  8.56 %
    Allowed  : 29.71 %
    Favored  : 61.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.21), residues: 1455
  helix: -0.23 (0.31), residues: 282
  sheet: -0.42 (0.33), residues: 253
  loop : -2.91 (0.18), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 126 
 TYR   0.014   0.002   TYR D1240 
 PHE   0.020   0.002   PHE A  40 
 TRP   0.015   0.002   TRP D1583 
 HIS   0.004   0.001   HIS B 435 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.20 (11839)
  covalent geometry    : angle       0.83176 /  0.42 (16041)
  SS BOND              : bond        0.00616 /  0.46 (   12)
  SS BOND              : angle       1.64662 /  0.99 (   24)
  hydrogen bonds       : bond        0.03961 /  2.69 (  310)
  hydrogen bonds       : angle       5.52040 /  3.92 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 115
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6897 (ttpp)
REVERT: A   61 MET cc_start: 0.7679 (mmt) cc_final: 0.6648 (mmm)
REVERT: A  155 GLN cc_start: 0.8156 (mp10) cc_final: 0.7831 (mp-120)
REVERT: A  164 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8396 (tm)
REVERT: B  348 PHE cc_start: 0.8500 (t80) cc_final: 0.8295 (t80)
REVERT: B  419 MET cc_start: 0.7600 (tmm) cc_final: 0.7222 (tmm)
REVERT: B  430 SER cc_start: 0.8766 (m) cc_final: 0.8480 (p)
REVERT: B  467 TYR cc_start: 0.6071 (p90) cc_final: 0.5835 (p90)
REVERT: B  508 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.5456 (tpt-90)
REVERT: B  557 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7173 (mp-120)
REVERT: D  804 MET cc_start: 0.6842 (tmm) cc_final: 0.6492 (tmm)
REVERT: D 1075 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.7699 (t)
REVERT: D 1301 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7195 (mp0)
REVERT: D 1379 SER cc_start: 0.6928 (OUTLIER) cc_final: 0.6725 (m)
REVERT: D 1445 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.6001 (m-80)
REVERT: D 1487 GLU cc_start: 0.8770 (pp20) cc_final: 0.8552 (tm-30)
REVERT: D 1541 MET cc_start: 0.6894 (mmt) cc_final: 0.6463 (tpp)
REVERT: D 1575 GLU cc_start: 0.8837 (tp30) cc_final: 0.8626 (tp30)
REVERT: D 1603 ASP cc_start: 0.8719 (m-30) cc_final: 0.7790 (t0)
  outliers start: 111
  outliers final: 45
  residues processed: 204
  average time/residue: 0.4272
  time to fit residues: 97.9453
Evaluate side-chains
  156 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 103
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  109 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  382 ASP
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  429 ASN
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  793 ILE
Chi-restraints excluded: chain D residue  802 THR
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  897 HIS
Chi-restraints excluded: chain D residue  914 ILE
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1263 ASP
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1301 GLU
Chi-restraints excluded: chain D residue 1379 SER
Chi-restraints excluded: chain D residue 1382 ASP
Chi-restraints excluded: chain D residue 1416 PHE
Chi-restraints excluded: chain D residue 1445 PHE
Chi-restraints excluded: chain D residue 1446 ASN
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1489 CYS
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 109 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 58 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0470
   chunk 12 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.5078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1277 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 = 0.4619 r_free = 0.4619 target = 0.115484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.099763 restraints weight = 61278.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 5.89
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6636
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11851  Z= 0.137
  Angle     :  0.792  14.707  16065  Z= 0.393
  Chirality :  0.047   0.263   1807
  Planarity :  0.005   0.061   2077
  Dihedral  :  6.677  57.991   1593
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 18.82
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.26 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 30.40 %
    Favored  : 63.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.21), residues: 1455
  helix:  0.02 (0.31), residues: 279
  sheet: -0.52 (0.33), residues: 258
  loop : -2.75 (0.19), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 551 
 TYR   0.013   0.001   TYR D1460 
 PHE   0.018   0.002   PHE B 617 
 TRP   0.014   0.001   TRP D1583 
 HIS   0.008   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 (11839)
  covalent geometry    : angle       0.79029 /  0.39 (16041)
  SS BOND              : bond        0.00595 /  0.45 (   12)
  SS BOND              : angle       1.58914 /  1.01 (   24)
  hydrogen bonds       : bond        0.03394 /  2.33 (  310)
  hydrogen bonds       : angle       5.25712 /  3.72 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 126
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6617 (ttpp)
REVERT: A   61 MET cc_start: 0.7379 (mmt) cc_final: 0.6242 (mmt)
REVERT: A  155 GLN cc_start: 0.8145 (mp10) cc_final: 0.7758 (mp-120)
REVERT: B  348 PHE cc_start: 0.8642 (t80) cc_final: 0.8310 (t80)
REVERT: B  419 MET cc_start: 0.7626 (tmm) cc_final: 0.7266 (tmm)
REVERT: B  430 SER cc_start: 0.8586 (m) cc_final: 0.8316 (p)
REVERT: B  495 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6669 (mp)
REVERT: B  508 ARG cc_start: 0.5699 (OUTLIER) cc_final: 0.5093 (ptp-170)
REVERT: B  557 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6915 (mp-120)
REVERT: D  804 MET cc_start: 0.6804 (tmm) cc_final: 0.4341 (mmp)
REVERT: D  899 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6277 (pt)
REVERT: D 1075 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7574 (t)
REVERT: D 1181 LYS cc_start: 0.7997 (pttt) cc_final: 0.7711 (mmtm)
REVERT: D 1414 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7315 (tptt)
REVERT: D 1445 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5335 (m-80)
REVERT: D 1487 GLU cc_start: 0.8721 (pp20) cc_final: 0.8496 (tm-30)
REVERT: D 1541 MET cc_start: 0.7033 (mmt) cc_final: 0.6599 (tpp)
REVERT: D 1575 GLU cc_start: 0.8802 (tp30) cc_final: 0.8564 (tp30)
REVERT: D 1603 ASP cc_start: 0.8683 (m-30) cc_final: 0.7918 (t0)
  outliers start: 85
  outliers final: 39
  residues processed: 196
  average time/residue: 0.4882
  time to fit residues: 106.2641
Evaluate side-chains
  155 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 108
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   40 PHE
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  392 HIS
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain C residue  666 LYS
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  802 THR
Chi-restraints excluded: chain D residue  897 HIS
Chi-restraints excluded: chain D residue  899 ILE
Chi-restraints excluded: chain D residue  914 ILE
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1378 MET
Chi-restraints excluded: chain D residue 1382 ASP
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1445 PHE
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1489 CYS
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0070
   chunk 8 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 98 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 66 optimal weight:    8.9990
   chunk 111 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 131 optimal weight:   20.0000
   overall best weight:    1.4002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1186 ASN
D1446 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.114134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.098278 restraints weight = 60807.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.4241 rms_B_bonded: 6.02
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11851  Z= 0.150
  Angle     :  0.797  12.131  16065  Z= 0.395
  Chirality :  0.047   0.263   1807
  Planarity :  0.005   0.060   2077
  Dihedral  :  6.501  58.895   1591
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 20.07
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.26 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 31.48 %
    Favored  : 61.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.21), residues: 1455
  helix:  0.02 (0.31), residues: 278
  sheet: -0.56 (0.33), residues: 262
  loop : -2.77 (0.19), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D1510 
 TYR   0.025   0.001   TYR B 467 
 PHE   0.013   0.001   PHE D 898 
 TRP   0.015   0.001   TRP D1583 
 HIS   0.007   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 (11839)
  covalent geometry    : angle       0.79583 /  0.39 (16041)
  SS BOND              : bond        0.00526 /  0.40 (   12)
  SS BOND              : angle       1.45558 /  0.93 (   24)
  hydrogen bonds       : bond        0.03493 /  2.38 (  310)
  hydrogen bonds       : angle       5.27173 /  3.75 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 121
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6777 (mm)
REVERT: A   51 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6738 (ttpp)
REVERT: A   61 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6182 (mmm)
REVERT: A  111 GLN cc_start: 0.5873 (OUTLIER) cc_final: 0.5513 (mt0)
REVERT: A  155 GLN cc_start: 0.8226 (mp10) cc_final: 0.7809 (mp-120)
REVERT: A  179 MET cc_start: 0.5302 (tpp) cc_final: 0.4917 (tpp)
REVERT: A  183 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8209 (mtpt)
REVERT: B  364 ARG cc_start: 0.9076 (tpm170) cc_final: 0.7298 (mmm160)
REVERT: B  419 MET cc_start: 0.7548 (tmm) cc_final: 0.7181 (tmm)
REVERT: B  430 SER cc_start: 0.8736 (m) cc_final: 0.8486 (p)
REVERT: B  508 ARG cc_start: 0.5671 (tpt170) cc_final: 0.5190 (mpt-90)
REVERT: B  557 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.6903 (mp-120)
REVERT: B  617 PHE cc_start: 0.2496 (OUTLIER) cc_final: 0.1900 (p90)
REVERT: D  804 MET cc_start: 0.6602 (tmm) cc_final: 0.6237 (tmm)
REVERT: D 1075 SER cc_start: 0.8284 (p) cc_final: 0.7661 (t)
REVERT: D 1181 LYS cc_start: 0.7994 (pttt) cc_final: 0.7698 (mmtm)
REVERT: D 1414 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7402 (tptt)
REVERT: D 1445 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5629 (m-80)
REVERT: D 1603 ASP cc_start: 0.8711 (m-30) cc_final: 0.7878 (t0)
  outliers start: 86
  outliers final: 40
  residues processed: 193
  average time/residue: 0.4810
  time to fit residues: 103.2362
Evaluate side-chains
  157 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  382 ASP
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  581 PHE
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  778 THR
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  802 THR
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  890 VAL
Chi-restraints excluded: chain D residue  897 HIS
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1378 MET
Chi-restraints excluded: chain D residue 1382 ASP
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1424 ILE
Chi-restraints excluded: chain D residue 1445 PHE
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 138 optimal weight:    9.9990
   chunk 99 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 123 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0970
   chunk 63 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   overall best weight:    1.4182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 558 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 = 0.4595 r_free = 0.4595 target = 0.114001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.098054 restraints weight = 60986.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 6.07
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11851  Z= 0.152
  Angle     :  0.807  11.009  16065  Z= 0.400
  Chirality :  0.047   0.254   1807
  Planarity :  0.005   0.094   2077
  Dihedral  :  6.467  58.142   1590
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 20.67
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.20 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 31.56 %
    Favored  : 60.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.21), residues: 1455
  helix:  0.02 (0.31), residues: 280
  sheet: -0.56 (0.33), residues: 262
  loop : -2.74 (0.19), residues: 913

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D1510 
 TYR   0.012   0.001   TYR D1460 
 PHE   0.028   0.002   PHE B 348 
 TRP   0.014   0.001   TRP D1583 
 HIS   0.007   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 (11839)
  covalent geometry    : angle       0.80577 /  0.40 (16041)
  SS BOND              : bond        0.00496 /  0.38 (   12)
  SS BOND              : angle       1.34162 /  0.89 (   24)
  hydrogen bonds       : bond        0.03407 /  2.32 (  310)
  hydrogen bonds       : angle       5.16638 /  3.66 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 109
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6668 (ttpp)
REVERT: A   61 MET cc_start: 0.7441 (mmt) cc_final: 0.6338 (mmm)
REVERT: A  111 GLN cc_start: 0.5738 (OUTLIER) cc_final: 0.5405 (mt0)
REVERT: A  155 GLN cc_start: 0.8148 (mp10) cc_final: 0.7735 (mp-120)
REVERT: A  170 SER cc_start: 0.8708 (m) cc_final: 0.8393 (p)
REVERT: A  179 MET cc_start: 0.5468 (tpp) cc_final: 0.5239 (tpp)
REVERT: B  419 MET cc_start: 0.7586 (tmm) cc_final: 0.7143 (tmm)
REVERT: B  430 SER cc_start: 0.8598 (m) cc_final: 0.8307 (p)
REVERT: B  495 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6505 (mp)
REVERT: B  508 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5145 (mpt-90)
REVERT: B  557 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6872 (mp-120)
REVERT: B  616 VAL cc_start: 0.4449 (OUTLIER) cc_final: 0.3656 (m)
REVERT: B  617 PHE cc_start: 0.2335 (OUTLIER) cc_final: 0.1690 (p90)
REVERT: D  747 GLU cc_start: 0.5227 (OUTLIER) cc_final: 0.3599 (tm-30)
REVERT: D  804 MET cc_start: 0.6547 (tmm) cc_final: 0.6147 (tmm)
REVERT: D 1008 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (pm20)
REVERT: D 1075 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7693 (t)
REVERT: D 1181 LYS cc_start: 0.8018 (pttt) cc_final: 0.7714 (mmtm)
REVERT: D 1315 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8550 (tptt)
REVERT: D 1414 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7376 (tptt)
REVERT: D 1603 ASP cc_start: 0.8724 (m-30) cc_final: 0.7895 (t0)
  outliers start: 99
  outliers final: 49
  residues processed: 191
  average time/residue: 0.4648
  time to fit residues: 99.2993
Evaluate side-chains
  167 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 106
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 HIS
Chi-restraints excluded: chain B residue  429 ASN
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  581 PHE
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain C residue  666 LYS
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  778 THR
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  825 ILE
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  890 VAL
Chi-restraints excluded: chain D residue  914 ILE
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1008 GLU
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1147 ILE
Chi-restraints excluded: chain D residue 1203 LYS
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1315 LYS
Chi-restraints excluded: chain D residue 1378 MET
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1597 SER
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 136 optimal weight:    9.9990
   chunk 82 optimal weight:    8.9990
   chunk 123 optimal weight:    1.9990
   chunk 96 optimal weight:    6.9990
   chunk 98 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 129 optimal weight:   10.0000
   chunk 132 optimal weight:    9.9990
   chunk 91 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 128 optimal weight:    0.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN
** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 558 GLN ** 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 = 0.4564 r_free = 0.4564 target = 0.112269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.096513 restraints weight = 60607.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 5.86
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6747
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11851  Z= 0.183
  Angle     :  0.828  10.733  16065  Z= 0.414
  Chirality :  0.048   0.238   1807
  Planarity :  0.006   0.094   2077
  Dihedral  :  6.572  58.852   1590
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 21.28
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.81 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  7.25 %
    Allowed  : 31.17 %
    Favored  : 61.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.21), residues: 1455
  helix: -0.07 (0.31), residues: 285
  sheet: -0.54 (0.33), residues: 261
  loop : -2.70 (0.19), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  13 
 TYR   0.026   0.002   TYR B 467 
 PHE   0.019   0.002   PHE A  40 
 TRP   0.016   0.001   TRP B 530 
 HIS   0.006   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 (11839)
  covalent geometry    : angle       0.82665 /  0.41 (16041)
  SS BOND              : bond        0.00512 /  0.38 (   12)
  SS BOND              : angle       1.50338 /  0.95 (   24)
  hydrogen bonds       : bond        0.03563 /  2.43 (  310)
  hydrogen bonds       : angle       5.24160 /  3.70 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 105
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6760 (ttpp)
REVERT: A   61 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.6629 (mmm)
REVERT: A  111 GLN cc_start: 0.5809 (OUTLIER) cc_final: 0.5430 (mt0)
REVERT: A  155 GLN cc_start: 0.8165 (mp10) cc_final: 0.7736 (mp-120)
REVERT: A  170 SER cc_start: 0.8746 (m) cc_final: 0.8503 (p)
REVERT: B  364 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7228 (mmm160)
REVERT: B  419 MET cc_start: 0.7522 (tmm) cc_final: 0.7159 (tmm)
REVERT: B  430 SER cc_start: 0.8764 (m) cc_final: 0.8482 (p)
REVERT: B  473 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5129 (mmm)
REVERT: B  508 ARG cc_start: 0.5716 (tpt170) cc_final: 0.5349 (mtt-85)
REVERT: B  557 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6839 (mp-120)
REVERT: B  616 VAL cc_start: 0.4542 (OUTLIER) cc_final: 0.3769 (m)
REVERT: B  617 PHE cc_start: 0.2502 (OUTLIER) cc_final: 0.1857 (p90)
REVERT: D  747 GLU cc_start: 0.5332 (OUTLIER) cc_final: 0.3738 (tm-30)
REVERT: D  804 MET cc_start: 0.6704 (tmm) cc_final: 0.6178 (tmm)
REVERT: D 1008 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8454 (pm20)
REVERT: D 1075 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7737 (t)
REVERT: D 1181 LYS cc_start: 0.8008 (pttt) cc_final: 0.7676 (mptt)
REVERT: D 1315 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8568 (tptt)
REVERT: D 1414 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7469 (tptt)
REVERT: D 1541 MET cc_start: 0.6639 (mpp) cc_final: 0.6128 (tpp)
REVERT: D 1603 ASP cc_start: 0.8723 (m-30) cc_final: 0.7961 (t0)
  outliers start: 94
  outliers final: 51
  residues processed: 183
  average time/residue: 0.4498
  time to fit residues: 92.2093
Evaluate side-chains
  167 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 103
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  132 HIS
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain C residue  666 LYS
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  778 THR
Chi-restraints excluded: chain D residue  783 LEU
Chi-restraints excluded: chain D residue  793 ILE
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  825 ILE
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  890 VAL
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1008 GLU
Chi-restraints excluded: chain D residue 1017 LEU
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1147 ILE
Chi-restraints excluded: chain D residue 1203 LYS
Chi-restraints excluded: chain D residue 1263 ASP
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1315 LYS
Chi-restraints excluded: chain D residue 1378 MET
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1424 ILE
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1597 SER
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 131 optimal weight:   30.0000
   chunk 60 optimal weight:    0.0030
   chunk 44 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0980
   chunk 108 optimal weight:    7.9990
   chunk 118 optimal weight:    5.9990
   chunk 35 optimal weight:    0.1980
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.2594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 558 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 = 0.4590 r_free = 0.4590 target = 0.113793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.098085 restraints weight = 60680.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 5.87
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11851  Z= 0.150
  Angle     :  0.813  10.822  16065  Z= 0.403
  Chirality :  0.047   0.231   1807
  Planarity :  0.005   0.085   2077
  Dihedral  :  6.441  58.904   1590
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.99 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 32.87 %
    Favored  : 61.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.21), residues: 1455
  helix:  0.03 (0.31), residues: 285
  sheet: -0.46 (0.34), residues: 256
  loop : -2.69 (0.19), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 508 
 TYR   0.012   0.001   TYR D1460 
 PHE   0.015   0.001   PHE A  40 
 TRP   0.052   0.002   TRP A 171 
 HIS   0.006   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (11839)
  covalent geometry    : angle       0.81158 /  0.40 (16041)
  SS BOND              : bond        0.00486 /  0.37 (   12)
  SS BOND              : angle       1.40134 /  0.86 (   24)
  hydrogen bonds       : bond        0.03359 /  2.29 (  310)
  hydrogen bonds       : angle       5.15366 /  3.63 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 109
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6663 (ttpp)
REVERT: A   61 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.5945 (mmm)
REVERT: A  111 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5304 (mt0)
REVERT: A  155 GLN cc_start: 0.8264 (mp10) cc_final: 0.7820 (mp-120)
REVERT: B  364 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7244 (mmm160)
REVERT: B  419 MET cc_start: 0.7450 (tmm) cc_final: 0.7128 (tmm)
REVERT: B  430 SER cc_start: 0.8710 (m) cc_final: 0.8424 (p)
REVERT: B  473 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.4854 (mmm)
REVERT: B  508 ARG cc_start: 0.5700 (tpt170) cc_final: 0.5442 (mpt-90)
REVERT: B  557 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.6824 (mp-120)
REVERT: B  616 VAL cc_start: 0.4735 (OUTLIER) cc_final: 0.3821 (m)
REVERT: B  617 PHE cc_start: 0.2278 (OUTLIER) cc_final: 0.1451 (p90)
REVERT: D  747 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.3613 (tm-30)
REVERT: D  804 MET cc_start: 0.6667 (tmm) cc_final: 0.6232 (tmm)
REVERT: D 1008 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8407 (pm20)
REVERT: D 1075 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7699 (t)
REVERT: D 1315 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8575 (tptt)
REVERT: D 1414 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7473 (tptt)
REVERT: D 1416 PHE cc_start: 0.7523 (p90) cc_final: 0.7281 (p90)
REVERT: D 1541 MET cc_start: 0.6616 (mpp) cc_final: 0.6108 (tpp)
REVERT: D 1603 ASP cc_start: 0.8689 (m-30) cc_final: 0.7965 (t0)
  outliers start: 73
  outliers final: 43
  residues processed: 171
  average time/residue: 0.4350
  time to fit residues: 82.8366
Evaluate side-chains
  159 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 103
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  107 TYR
Chi-restraints excluded: chain A residue  111 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  473 MET
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  557 GLN
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  581 PHE
Chi-restraints excluded: chain B residue  616 VAL
Chi-restraints excluded: chain B residue  617 PHE
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  778 THR
Chi-restraints excluded: chain D residue  793 ILE
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  890 VAL
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1008 GLU
Chi-restraints excluded: chain D residue 1073 ILE
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1203 LYS
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1315 LYS
Chi-restraints excluded: chain D residue 1378 MET
Chi-restraints excluded: chain D residue 1382 ASP
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1424 ILE
Chi-restraints excluded: chain D residue 1486 ASP
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1597 SER
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 103 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0000
   chunk 26 optimal weight:   10.0000
   chunk 108 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0030
   chunk 50 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.4794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 ASN
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 631 GLN
D1186 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.116070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.100328 restraints weight = 59971.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4278 rms_B_bonded: 6.12
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11851  Z= 0.138
  Angle     :  0.832  13.145  16065  Z= 0.407
  Chirality :  0.047   0.210   1807
  Planarity :  0.005   0.080   2077
  Dihedral  :  6.235  59.153   1588
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.37 %
    Favored  : 87.49 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 33.72 %
    Favored  : 61.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.22), residues: 1455
  helix:  0.35 (0.32), residues: 273
  sheet: -0.56 (0.33), residues: 264
  loop : -2.62 (0.19), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D1510 
 TYR   0.027   0.001   TYR B 467 
 PHE   0.019   0.001   PHE A 196 
 TRP   0.052   0.002   TRP A 171 
 HIS   0.005   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (11839)
  covalent geometry    : angle       0.83080 /  0.41 (16041)
  SS BOND              : bond        0.00439 /  0.33 (   12)
  SS BOND              : angle       1.32501 /  0.82 (   24)
  hydrogen bonds       : bond        0.03211 /  2.18 (  310)
  hydrogen bonds       : angle       5.05014 /  3.56 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 121
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6541 (ttpp)
REVERT: A   61 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6245 (mmt)
REVERT: A  154 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6592 (ttpt)
REVERT: B  419 MET cc_start: 0.7461 (tmm) cc_final: 0.7132 (tmm)
REVERT: B  430 SER cc_start: 0.8631 (m) cc_final: 0.8350 (p)
REVERT: B  495 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6239 (mp)
REVERT: B  508 ARG cc_start: 0.5674 (tpt170) cc_final: 0.5317 (pmm-80)
REVERT: D  747 GLU cc_start: 0.4959 (OUTLIER) cc_final: 0.3188 (tm-30)
REVERT: D  804 MET cc_start: 0.6460 (tmm) cc_final: 0.4067 (mmt)
REVERT: D 1008 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8412 (pm20)
REVERT: D 1075 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7660 (t)
REVERT: D 1181 LYS cc_start: 0.8006 (pttt) cc_final: 0.7698 (mmtm)
REVERT: D 1414 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7273 (tptt)
REVERT: D 1416 PHE cc_start: 0.7348 (p90) cc_final: 0.7100 (p90)
REVERT: D 1541 MET cc_start: 0.6497 (mpp) cc_final: 0.6060 (tpp)
REVERT: D 1603 ASP cc_start: 0.8685 (m-30) cc_final: 0.7946 (t0)
  outliers start: 59
  outliers final: 34
  residues processed: 167
  average time/residue: 0.4585
  time to fit residues: 84.8561
Evaluate side-chains
  154 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  581 PHE
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  793 ILE
Chi-restraints excluded: chain D residue  825 ILE
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue  914 ILE
Chi-restraints excluded: chain D residue  951 ASP
Chi-restraints excluded: chain D residue 1008 GLU
Chi-restraints excluded: chain D residue 1075 SER
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1506 THR
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1597 SER
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 90 optimal weight:   20.0000
   chunk 88 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0770
   chunk 28 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 132 optimal weight:   10.0000
   chunk 79 optimal weight:    0.4980
   chunk 33 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 ASN
** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 822 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.116197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.100570 restraints weight = 60163.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.4282 rms_B_bonded: 5.98
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11851  Z= 0.137
  Angle     :  0.835  11.737  16065  Z= 0.410
  Chirality :  0.047   0.205   1807
  Planarity :  0.005   0.080   2077
  Dihedral  :  6.163  57.802   1588
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.55 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 34.03 %
    Favored  : 62.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.22), residues: 1455
  helix:  0.38 (0.32), residues: 273
  sheet: -0.57 (0.33), residues: 267
  loop : -2.60 (0.19), residues: 915

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 403 
 TYR   0.010   0.001   TYR D1460 
 PHE   0.023   0.001   PHE B 348 
 TRP   0.041   0.002   TRP A 171 
 HIS   0.004   0.001   HIS A  38 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 (11839)
  covalent geometry    : angle       0.83363 /  0.41 (16041)
  SS BOND              : bond        0.00440 /  0.33 (   12)
  SS BOND              : angle       1.34284 /  0.85 (   24)
  hydrogen bonds       : bond        0.03168 /  2.14 (  310)
  hydrogen bonds       : angle       5.03184 /  3.54 (  840)

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

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

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2910 Ramachandran restraints generated.
    1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6485 (ttpp)
REVERT: A   61 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6131 (mmt)
REVERT: A  154 LYS cc_start: 0.7273 (ttpt) cc_final: 0.6951 (ttpt)
REVERT: A  183 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8240 (mtpt)
REVERT: B  346 MET cc_start: 0.5832 (OUTLIER) cc_final: 0.5527 (mmm)
REVERT: B  419 MET cc_start: 0.7445 (tmm) cc_final: 0.7121 (tmm)
REVERT: B  430 SER cc_start: 0.8562 (m) cc_final: 0.8278 (p)
REVERT: B  495 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6318 (mp)
REVERT: B  508 ARG cc_start: 0.5661 (tpt170) cc_final: 0.5339 (pmm-80)
REVERT: D  747 GLU cc_start: 0.4938 (OUTLIER) cc_final: 0.3066 (tm-30)
REVERT: D  800 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.3074 (mp0)
REVERT: D  804 MET cc_start: 0.6481 (tmm) cc_final: 0.6030 (tmm)
REVERT: D 1008 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8376 (pm20)
REVERT: D 1075 SER cc_start: 0.8259 (p) cc_final: 0.7662 (t)
REVERT: D 1181 LYS cc_start: 0.7989 (pttt) cc_final: 0.7688 (mmtm)
REVERT: D 1414 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7282 (tptt)
REVERT: D 1416 PHE cc_start: 0.7331 (p90) cc_final: 0.7091 (p90)
REVERT: D 1541 MET cc_start: 0.6561 (mpp) cc_final: 0.6310 (tpp)
REVERT: D 1603 ASP cc_start: 0.8648 (m-30) cc_final: 0.7985 (t0)
  outliers start: 50
  outliers final: 31
  residues processed: 158
  average time/residue: 0.4416
  time to fit residues: 77.4414
Evaluate side-chains
  154 residues out of total 1296 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 115
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   77 GLU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  147 ASN
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  338 THR
Chi-restraints excluded: chain B residue  346 MET
Chi-restraints excluded: chain B residue  364 ARG
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  510 VAL
Chi-restraints excluded: chain B residue  531 VAL
Chi-restraints excluded: chain B residue  535 ASP
Chi-restraints excluded: chain B residue  542 VAL
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  581 PHE
Chi-restraints excluded: chain C residue  692 ILE
Chi-restraints excluded: chain D residue  747 GLU
Chi-restraints excluded: chain D residue  770 ASN
Chi-restraints excluded: chain D residue  793 ILE
Chi-restraints excluded: chain D residue  800 GLU
Chi-restraints excluded: chain D residue  825 ILE
Chi-restraints excluded: chain D residue  888 VAL
Chi-restraints excluded: chain D residue 1008 GLU
Chi-restraints excluded: chain D residue 1077 VAL
Chi-restraints excluded: chain D residue 1278 LEU
Chi-restraints excluded: chain D residue 1280 SER
Chi-restraints excluded: chain D residue 1414 LYS
Chi-restraints excluded: chain D residue 1489 CYS
Chi-restraints excluded: chain D residue 1519 VAL
Chi-restraints excluded: chain D residue 1532 LEU
Chi-restraints excluded: chain D residue 1597 SER
Chi-restraints excluded: chain D residue 1627 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 58 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 131 optimal weight:   30.0000
   chunk 100 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 127 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    4.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 ASN
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1186 ASN
D1268 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.109456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.093455 restraints weight = 60669.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 5.82
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6841
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  11851  Z= 0.289
  Angle     :  0.962  13.601  16065  Z= 0.482
  Chirality :  0.051   0.247   1807
  Planarity :  0.007   0.101   2077
  Dihedral  :  6.907  57.555   1587
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 26.89
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 14.91 %
    Favored  : 84.88 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 33.72 %
    Favored  : 61.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.21), residues: 1455
  helix: -0.05 (0.31), residues: 278
  sheet: -0.63 (0.33), residues: 261
  loop : -2.75 (0.19), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  13 
 TYR   0.022   0.002   TYR B 467 
 PHE   0.029   0.003   PHE D 898 
 TRP   0.031   0.002   TRP A 182 
 HIS   0.005   0.001   HIS D1608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00662 /  0.29 (11839)
  covalent geometry    : angle       0.96019 /  0.48 (16041)
  SS BOND              : bond        0.00599 /  0.43 (   12)
  SS BOND              : angle       1.70907 /  1.07 (   24)
  hydrogen bonds       : bond        0.04145 /  2.84 (  310)
  hydrogen bonds       : angle       5.42098 /  3.79 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4852.80 seconds
wall clock time: 83 minutes 41.70 seconds (5021.70 seconds total)