Starting phenix.real_space_refine
on Wed Mar  4 02:38:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xjb_22205/03_2026/6xjb_22205.cif"
  }
  resolution = 3.8
  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=   0.001
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      18      5.16       5
     C    6352      2.51       5
     N    1711      2.21       5
     O    1989      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10070
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10070
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1277, 10070
          Classifications: {'peptide': 1277}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 33, 'TRANS': 1243}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 2.47, per 1000 atoms: 0.25
  Number of scatterers: 10070
  At special positions: 0
  Unit cell: (94.176, 110.592, 125.28, 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      18     16.00
     O    1989      8.00
     N    1711      7.00
     C    6352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 526.3 milliseconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 17 sheets defined
      33.7% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 782 through 793
      removed outlier: 3.807A  pdb=" N   LYS A 788 " --> pdb=" O   SER A 784 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASN A 791 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN A 792 " --> pdb=" O   LYS A 788 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN A 793 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1015
      removed outlier: 4.326A  pdb=" N   GLY A1015 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1083
      removed outlier: 3.718A  pdb=" N   VAL A1082 " --> pdb=" O   SER A1079 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   SER A1083 " --> pdb=" O   GLN A1080 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1079 through 1083'
    Processing helix  chain 'A' and resid 1119 through 1128
      removed outlier: 3.593A  pdb=" N   LYS A1128 " --> pdb=" O   LYS A1124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1134 through 1143
    Processing helix  chain 'A' and resid 1169 through 1174
    Processing helix  chain 'A' and resid 1211 through 1213
      No H-bonds generated for 'chain 'A' and resid 1211 through 1213'
    Processing helix  chain 'A' and resid 1224 through 1238
      removed outlier: 4.173A  pdb=" N   ILE A1228 " --> pdb=" O   ASP A1224 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLU A1231 " --> pdb=" O   SER A1227 " (cutoff:3.500A)
      Proline residue:  A1234  - end of helix
      removed outlier: 3.598A  pdb=" N   LYS A1238 " --> pdb=" O   PRO A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1243 through 1250
      removed outlier: 3.540A  pdb=" N   ARG A1247 " --> pdb=" O   SER A1243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1263 through 1273
    Processing helix  chain 'A' and resid 1273 through 1286
      removed outlier: 3.935A  pdb=" N   SER A1277 " --> pdb=" O   ASN A1273 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ALA A1286 " --> pdb=" O   LEU A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1306
      removed outlier: 4.482A  pdb=" N   ARG A1296 " --> pdb=" O   ASN A1292 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASN A1306 " --> pdb=" O   LYS A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1321
    Processing helix  chain 'A' and resid 1330 through 1335
      removed outlier: 3.640A  pdb=" N   MET A1335 " --> pdb=" O   LYS A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1357
    Processing helix  chain 'A' and resid 1364 through 1366
      No H-bonds generated for 'chain 'A' and resid 1364 through 1366'
    Processing helix  chain 'A' and resid 1367 through 1375
      removed outlier: 3.537A  pdb=" N   TYR A1372 " --> pdb=" O   ASN A1368 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   GLY A1373 " --> pdb=" O   VAL A1369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1384 through 1396
    Processing helix  chain 'A' and resid 1401 through 1410
    Processing helix  chain 'A' and resid 1421 through 1430
      removed outlier: 3.501A  pdb=" N   GLY A1429 " --> pdb=" O   LYS A1425 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU A1430 " --> pdb=" O   THR A1426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1438 through 1444
    Processing helix  chain 'A' and resid 1450 through 1452
      No H-bonds generated for 'chain 'A' and resid 1450 through 1452'
    Processing helix  chain 'A' and resid 1453 through 1459
      removed outlier: 3.533A  pdb=" N   THR A1459 " --> pdb=" O   LEU A1455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1480 through 1482
      No H-bonds generated for 'chain 'A' and resid 1480 through 1482'
    Processing helix  chain 'A' and resid 1491 through 1519
      removed outlier: 3.521A  pdb=" N   ASP A1495 " --> pdb=" O   LYS A1491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1523 through 1527
    Processing helix  chain 'A' and resid 1558 through 1564
    Processing helix  chain 'A' and resid 1595 through 1610
      removed outlier: 3.864A  pdb=" N   ALA A1599 " --> pdb=" O   ASP A1595 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ILE A1600 " --> pdb=" O   LYS A1596 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A1601 " --> pdb=" O   ASP A1597 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   HIS A1604 " --> pdb=" O   ILE A1600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1628 through 1633
      removed outlier: 3.552A  pdb=" N   LYS A1632 " --> pdb=" O   GLU A1628 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLY A1633 " --> pdb=" O   PHE A1629 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1628 through 1633'
    Processing helix  chain 'A' and resid 1658 through 1662
      removed outlier: 3.564A  pdb=" N   GLU A1661 " --> pdb=" O   ASP A1658 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY A1662 " --> pdb=" O   SER A1659 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1658 through 1662'
    Processing helix  chain 'A' and resid 1676 through 1705
    Processing helix  chain 'A' and resid 1707 through 1714
      removed outlier: 3.628A  pdb=" N   ALA A1713 " --> pdb=" O   TYR A1709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1742 through 1749
      removed outlier: 3.530A  pdb=" N   ASN A1748 " --> pdb=" O   ALA A1744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1751 through 1758
      removed outlier: 3.546A  pdb=" N   ILE A1756 " --> pdb=" O   PHE A1752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1798 through 1812
      removed outlier: 3.679A  pdb=" N   ARG A1803 " --> pdb=" O   LEU A1799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1817 through 1823
    Processing helix  chain 'A' and resid 1826 through 1834
    Processing helix  chain 'A' and resid 1848 through 1857
    Processing helix  chain 'A' and resid 1863 through 1880
    Processing helix  chain 'A' and resid 1904 through 1921
      removed outlier: 3.656A  pdb=" N   LEU A1908 " --> pdb=" O   ASN A1904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1934 through 1951
      removed outlier: 3.652A  pdb=" N   THR A1951 " --> pdb=" O   TYR A1947 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 680 through 681
      removed outlier: 6.262A  pdb=" N   LEU A 680 " --> pdb=" O   GLN A 754 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLU A 756 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 699 through 700
      removed outlier: 3.895A  pdb=" N   ARG A 699 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 736 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL A 743 " --> pdb=" O   GLU A 736 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   PHE A 765 " --> pdb=" O   ALA A 748 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 699 through 700
      removed outlier: 3.895A  pdb=" N   ARG A 699 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 797 through 799
      removed outlier: 6.043A  pdb=" N   TYR A 798 " --> pdb=" O   GLY A 829 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   THR A 853 " --> pdb=" O   ILE A 828 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 804 through 805
      removed outlier: 6.831A  pdb=" N   LEU A 804 " --> pdb=" O   TYR A 839 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LYS A 860 " --> pdb=" O   ILE A 838 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   SER A 858 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP A 889 " --> pdb=" O   SER A 858 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LYS A 860 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL A 891 " --> pdb=" O   LYS A 860 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   VAL A 862 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ALA A 893 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ILE A 864 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   VAL A 920 " --> pdb=" O   GLY A 890 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LEU A 892 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ILE A 919 " --> pdb=" O   SER A 955 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   ASP A 986 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   SER A 956 " --> pdb=" O   ASP A 986 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 804 through 805
      removed outlier: 6.831A  pdb=" N   LEU A 804 " --> pdb=" O   TYR A 839 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LYS A 860 " --> pdb=" O   ILE A 838 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   SER A 858 " --> pdb=" O   HIS A 887 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP A 889 " --> pdb=" O   SER A 858 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LYS A 860 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   VAL A 891 " --> pdb=" O   LYS A 860 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   VAL A 862 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   ALA A 893 " --> pdb=" O   VAL A 862 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ILE A 864 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 848 through 849
      removed outlier: 6.935A  pdb=" N   ASN A 875 " --> pdb=" O   LEU A 902 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 870 through 871
      removed outlier: 6.412A  pdb=" N   ILE A 870 " --> pdb=" O   GLY A 899 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 882 through 884
      removed outlier: 6.353A  pdb=" N   ILE A 883 " --> pdb=" O   ALA A 911 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   ILE A 945 " --> pdb=" O   GLN A 979 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 930 through 931
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1053 through 1055
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1159 through 1161
      removed outlier: 3.765A  pdb=" N   LYS A1196 " --> pdb=" O   ASN A1208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1324 through 1325
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1413 through 1417
      removed outlier: 3.696A  pdb=" N   GLU A1417 " --> pdb=" O   SER A1469 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1533 through 1534
      removed outlier: 7.413A  pdb=" N   TYR A1534 " --> pdb=" O   TYR A1588 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1734 through 1739
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1836 through 1839

    323 hydrogen bonds defined for protein.
    927 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: 2.05

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3333
        1.34 -     1.46: 1781
        1.46 -     1.57: 5109
        1.57 -     1.69: 0
        1.69 -     1.80: 36
  Bond restraints: 10259
  Sorted by residual:
  bond pdb=" N   THR A1057 "
       pdb=" CA  THR A1057 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.72e+00
  bond pdb=" N   THR A1901 "
       pdb=" CA  THR A1901 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.16e+00
  bond pdb=" N   VAL A1568 "
       pdb=" CA  VAL A1568 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.25e-02 6.40e+03 1.07e+00
  bond pdb=" N   ALA A1113 "
       pdb=" CA  ALA A1113 "
    ideal  model  delta    sigma   weight residual
    1.459  1.470 -0.012 1.16e-02 7.43e+03 1.04e+00
  bond pdb=" N   PRO A1098 "
       pdb=" CA  PRO A1098 "
    ideal  model  delta    sigma   weight residual
    1.471  1.459  0.013 1.29e-02 6.01e+03 9.55e-01
  ... (remaining 10254 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 13630
        1.69 -     3.37: 201
        3.37 -     5.06: 25
        5.06 -     6.74: 6
        6.74 -     8.43: 3
  Bond angle restraints: 13865
  Sorted by residual:
  angle pdb=" N   PRO A1094 "
        pdb=" CA  PRO A1094 "
        pdb=" CB  PRO A1094 "
      ideal   model   delta    sigma   weight residual
     103.27  110.21   -6.94 9.00e-01 1.23e+00 5.94e+01
  angle pdb=" N   PRO A1090 "
        pdb=" CA  PRO A1090 "
        pdb=" CB  PRO A1090 "
      ideal   model   delta    sigma   weight residual
     103.33  110.44   -7.11 9.30e-01 1.16e+00 5.84e+01
  angle pdb=" N   PRO A1098 "
        pdb=" CA  PRO A1098 "
        pdb=" CB  PRO A1098 "
      ideal   model   delta    sigma   weight residual
     103.44  110.07   -6.63 1.12e+00 7.97e-01 3.50e+01
  angle pdb=" C   TYR A1928 "
        pdb=" CA  TYR A1928 "
        pdb=" CB  TYR A1928 "
      ideal   model   delta    sigma   weight residual
     115.79  110.30    5.49 1.19e+00 7.06e-01 2.13e+01
  angle pdb=" C   PRO A1670 "
        pdb=" N   THR A1671 "
        pdb=" CA  THR A1671 "
      ideal   model   delta    sigma   weight residual
     121.54  129.97   -8.43 1.91e+00 2.74e-01 1.95e+01
  ... (remaining 13860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 5634
       17.56 -    35.12: 433
       35.12 -    52.68: 76
       52.68 -    70.25: 17
       70.25 -    87.81: 7
  Dihedral angle restraints: 6167
    sinusoidal: 2437
      harmonic: 3730
  Sorted by residual:
  dihedral pdb=" CA  ASP A1669 "
           pdb=" CB  ASP A1669 "
           pdb=" CG  ASP A1669 "
           pdb=" OD1 ASP A1669 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.11   58.11     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  ASP A1609 "
           pdb=" CB  ASP A1609 "
           pdb=" CG  ASP A1609 "
           pdb=" OD1 ASP A1609 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.98   57.98     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CB  GLU A1850 "
           pdb=" CG  GLU A1850 "
           pdb=" CD  GLU A1850 "
           pdb=" OE1 GLU A1850 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.81  -87.81     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 6164 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1209
       0.045 -    0.091: 242
       0.091 -    0.136: 67
       0.136 -    0.181: 2
       0.181 -    0.226: 3
  Chirality restraints: 1523
  Sorted by residual:
  chirality pdb=" CA  PRO A1098 "
            pdb=" N   PRO A1098 "
            pdb=" C   PRO A1098 "
            pdb=" CB  PRO A1098 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  PRO A1090 "
            pdb=" N   PRO A1090 "
            pdb=" C   PRO A1090 "
            pdb=" CB  PRO A1090 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  PRO A1094 "
            pdb=" N   PRO A1094 "
            pdb=" C   PRO A1094 "
            pdb=" CB  PRO A1094 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.80e-01
  ... (remaining 1520 not shown)

  Planarity restraints: 1803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 707 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO A 708 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 708 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 708 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1892 "   -0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO A1893 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A1893 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A1893 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1879 "   -0.010 2.00e-02 2.50e+03   9.58e-03 1.61e+00
        pdb=" CG  PHE A1879 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1879 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1879 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1879 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1879 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1879 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1800 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 296
        2.71 -     3.26: 10494
        3.26 -     3.81: 15967
        3.81 -     4.35: 20478
        4.35 -     4.90: 34592
  Nonbonded interactions: 81827
  Sorted by model distance:
  nonbonded pdb=" O   GLU A1059 "
            pdb=" ND2 ASN A1575 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" OG1 THR A 881 "
            pdb=" OG  SER A 908 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG  SER A1707 "
            pdb=" OE1 GLN A1710 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ASN A 793 "
            pdb=" OH  TYR A 798 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   SER A1751 "
            pdb=" OG  SER A1754 "
     model   vdw
     2.258 3.040
  ... (remaining 81822 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.680
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.260
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.002   0.047  10259  Z= 0.132
  Angle     :  0.561   8.428  13865  Z= 0.357
  Chirality :  0.040   0.226   1523
  Planarity :  0.003   0.037   1803
  Dihedral  : 13.114  87.806   3787
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -3.06 (0.20), residues: 1273
  helix: -1.26 (0.22), residues: 406
  sheet: -1.53 (0.37), residues: 174
  loop : -2.73 (0.19), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1225 
 TYR   0.010   0.001   TYR A1512 
 PHE   0.021   0.001   PHE A1879 
 TRP   0.005   0.001   TRP A1405 
 HIS   0.003   0.001   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (10259)
  covalent geometry    : angle       0.56051 (13865)
  hydrogen bonds       : bond        0.16796 (  311)
  hydrogen bonds       : angle       6.38537 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.7961 (p90) cc_final: 0.7659 (p90)
REVERT: A 1594 LEU cc_start: 0.8792 (mp) cc_final: 0.8567 (mp)
REVERT: A 1800 MET cc_start: 0.7970 (tpp) cc_final: 0.7719 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1139
  time to fit residues: 24.2432
Evaluate side-chains
  67 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 868 ASN
A 879 ASN
A1337 HIS
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1832 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.073932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.061739 restraints weight = 30337.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.063926 restraints weight = 15393.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.065407 restraints weight = 9710.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.066430 restraints weight = 6991.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.067028 restraints weight = 5500.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.091  10259  Z= 0.324
  Angle     :  0.718   8.530  13865  Z= 0.380
  Chirality :  0.046   0.153   1523
  Planarity :  0.004   0.060   1803
  Dihedral  :  4.948  20.770   1394
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.78 %
    Favored  : 85.44 %
  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: -2.27 (0.22), residues: 1273
  helix: -0.14 (0.25), residues: 413
  sheet: -1.41 (0.34), residues: 196
  loop : -2.50 (0.21), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1072 
 TYR   0.031   0.002   TYR A 982 
 PHE   0.030   0.003   PHE A1879 
 TRP   0.007   0.002   TRP A1448 
 HIS   0.008   0.001   HIS A1654 

Details of bonding type rmsd
  covalent geometry    : bond        0.00737 (10259)
  covalent geometry    : angle       0.71824 (13865)
  hydrogen bonds       : bond        0.04574 (  311)
  hydrogen bonds       : angle       5.06496 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8432 (p90) cc_final: 0.7805 (p90)
REVERT: A 1594 LEU cc_start: 0.9261 (mp) cc_final: 0.8973 (mp)
REVERT: A 1679 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7342 (t0)
REVERT: A 1712 MET cc_start: 0.7363 (mtt) cc_final: 0.7060 (mtm)
REVERT: A 1800 MET cc_start: 0.8288 (tpp) cc_final: 0.7652 (tpp)
REVERT: A 1827 GLU cc_start: 0.7410 (tt0) cc_final: 0.7073 (mt-10)
REVERT: A 1871 MET cc_start: 0.8601 (mtp) cc_final: 0.8188 (mtp)
  outliers start: 30
  outliers final: 18
  residues processed: 100
  average time/residue: 0.0966
  time to fit residues: 14.0178
Evaluate side-chains
  77 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  948 SER
Chi-restraints excluded: chain A residue  986 ASP
Chi-restraints excluded: chain A residue 1111 LYS
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1927 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 112 optimal weight:    0.8980
   chunk 9 optimal weight:    0.3980
   chunk 101 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 122 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1337 HIS
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1608 HIS
A1654 HIS
A1730 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.076473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.064348 restraints weight = 29794.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066655 restraints weight = 14823.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.068226 restraints weight = 9195.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.069276 restraints weight = 6511.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.070018 restraints weight = 5055.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10259  Z= 0.127
  Angle     :  0.547   7.195  13865  Z= 0.292
  Chirality :  0.041   0.155   1523
  Planarity :  0.004   0.052   1803
  Dihedral  :  4.596  19.825   1394
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.64 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.22), residues: 1273
  helix:  0.38 (0.26), residues: 410
  sheet: -1.24 (0.35), residues: 196
  loop : -2.38 (0.21), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1072 
 TYR   0.019   0.001   TYR A1947 
 PHE   0.026   0.001   PHE A1879 
 TRP   0.008   0.001   TRP A1405 
 HIS   0.003   0.001   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10259)
  covalent geometry    : angle       0.54658 (13865)
  hydrogen bonds       : bond        0.03606 (  311)
  hydrogen bonds       : angle       4.57120 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8495 (p90) cc_final: 0.7805 (p90)
REVERT: A 1085 LYS cc_start: 0.6393 (tptt) cc_final: 0.6183 (tppt)
REVERT: A 1193 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8231 (m-80)
REVERT: A 1444 THR cc_start: 0.9550 (p) cc_final: 0.9283 (p)
REVERT: A 1594 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8854 (mp)
REVERT: A 1605 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7665 (mm-30)
REVERT: A 1679 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7255 (t0)
REVERT: A 1698 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7314 (tm-30)
REVERT: A 1712 MET cc_start: 0.7367 (mtt) cc_final: 0.7088 (mtm)
REVERT: A 1800 MET cc_start: 0.8123 (tpp) cc_final: 0.7572 (tpp)
  outliers start: 29
  outliers final: 19
  residues processed: 95
  average time/residue: 0.1013
  time to fit residues: 13.8072
Evaluate side-chains
  87 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  979 GLN
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1193 PHE
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1899 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 102 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A1337 HIS
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.075039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.062767 restraints weight = 30211.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.065046 restraints weight = 15336.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.066595 restraints weight = 9588.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.067645 restraints weight = 6833.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.068373 restraints weight = 5336.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10259  Z= 0.184
  Angle     :  0.570   6.948  13865  Z= 0.303
  Chirality :  0.042   0.154   1523
  Planarity :  0.004   0.058   1803
  Dihedral  :  4.678  20.504   1394
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 13.73 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.22), residues: 1273
  helix:  0.57 (0.26), residues: 410
  sheet: -1.25 (0.37), residues: 187
  loop : -2.32 (0.21), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1529 
 TYR   0.017   0.001   TYR A1947 
 PHE   0.024   0.002   PHE A1879 
 TRP   0.007   0.001   TRP A1515 
 HIS   0.003   0.001   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (10259)
  covalent geometry    : angle       0.56987 (13865)
  hydrogen bonds       : bond        0.03646 (  311)
  hydrogen bonds       : angle       4.54377 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 69
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8511 (p90) cc_final: 0.7835 (p-80)
REVERT: A 1193 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8120 (m-80)
REVERT: A 1594 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8916 (mp)
REVERT: A 1605 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: A 1679 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7314 (t0)
REVERT: A 1698 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7014 (tm-30)
REVERT: A 1712 MET cc_start: 0.7454 (mtt) cc_final: 0.7205 (mtm)
REVERT: A 1800 MET cc_start: 0.8328 (tpp) cc_final: 0.7620 (tpp)
REVERT: A 1871 MET cc_start: 0.8349 (mtp) cc_final: 0.7954 (mtp)
  outliers start: 39
  outliers final: 28
  residues processed: 101
  average time/residue: 0.0946
  time to fit residues: 13.8916
Evaluate side-chains
  87 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 56
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  979 GLN
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1193 PHE
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1947 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A1337 HIS
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1608 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.076270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.064039 restraints weight = 29999.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.066371 restraints weight = 15048.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.067936 restraints weight = 9373.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.069009 restraints weight = 6641.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.069731 restraints weight = 5153.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10259  Z= 0.126
  Angle     :  0.530   7.658  13865  Z= 0.284
  Chirality :  0.040   0.162   1523
  Planarity :  0.004   0.072   1803
  Dihedral  :  4.541  19.343   1394
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 14.10 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.22), residues: 1273
  helix:  0.69 (0.26), residues: 410
  sheet: -1.08 (0.37), residues: 184
  loop : -2.30 (0.21), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1225 
 TYR   0.019   0.001   TYR A1197 
 PHE   0.023   0.001   PHE A1879 
 TRP   0.007   0.001   TRP A1405 
 HIS   0.003   0.000   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (10259)
  covalent geometry    : angle       0.53036 (13865)
  hydrogen bonds       : bond        0.03304 (  311)
  hydrogen bonds       : angle       4.36814 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 69
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8510 (p90) cc_final: 0.7809 (p-80)
REVERT: A 1193 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8216 (m-80)
REVERT: A 1241 TYR cc_start: 0.8647 (t80) cc_final: 0.8258 (t80)
REVERT: A 1444 THR cc_start: 0.9555 (p) cc_final: 0.9304 (p)
REVERT: A 1594 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8902 (mp)
REVERT: A 1605 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: A 1679 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7271 (t0)
REVERT: A 1698 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7126 (tm-30)
REVERT: A 1800 MET cc_start: 0.8298 (tpp) cc_final: 0.7561 (tpp)
  outliers start: 42
  outliers final: 27
  residues processed: 103
  average time/residue: 0.0910
  time to fit residues: 14.0455
Evaluate side-chains
  95 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 65
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  979 GLN
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1193 PHE
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1947 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 117 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A1237 GLN
A1337 HIS
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** 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 = 0.3148 r_free = 0.3148 target = 0.071711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.059568 restraints weight = 31078.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.061732 restraints weight = 15902.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.063179 restraints weight = 10039.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.064158 restraints weight = 7234.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.064874 restraints weight = 5725.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.076  10259  Z= 0.337
  Angle     :  0.716   7.664  13865  Z= 0.376
  Chirality :  0.046   0.181   1523
  Planarity :  0.004   0.043   1803
  Dihedral  :  5.180  22.343   1394
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 14.75 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.22), residues: 1273
  helix:  0.53 (0.26), residues: 405
  sheet: -1.21 (0.39), residues: 168
  loop : -2.37 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1225 
 TYR   0.024   0.002   TYR A 982 
 PHE   0.025   0.002   PHE A1879 
 TRP   0.010   0.002   TRP A1448 
 HIS   0.006   0.001   HIS A1608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00765 (10259)
  covalent geometry    : angle       0.71581 (13865)
  hydrogen bonds       : bond        0.04275 (  311)
  hydrogen bonds       : angle       4.83967 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 58
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  979 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7801 (mp10)
REVERT: A 1171 ILE cc_start: 0.8820 (tp) cc_final: 0.8474 (pt)
REVERT: A 1594 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8997 (mp)
REVERT: A 1605 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7868 (mm-30)
REVERT: A 1654 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7648 (p90)
REVERT: A 1679 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7421 (t0)
REVERT: A 1698 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7297 (tm-30)
REVERT: A 1800 MET cc_start: 0.8390 (tpp) cc_final: 0.7748 (tpp)
REVERT: A 1871 MET cc_start: 0.8392 (mtp) cc_final: 0.8173 (mtp)
REVERT: A 1953 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8278 (m-30)
  outliers start: 49
  outliers final: 36
  residues processed: 100
  average time/residue: 0.0870
  time to fit residues: 12.8370
Evaluate side-chains
  96 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 55
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  954 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  979 GLN
Chi-restraints excluded: chain A residue 1024 VAL
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1256 VAL
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1899 THR
Chi-restraints excluded: chain A residue 1947 TYR
Chi-restraints excluded: chain A residue 1953 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 115 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** 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 = 0.3200 r_free = 0.3200 target = 0.074264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.062043 restraints weight = 30294.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.064303 restraints weight = 15422.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.065833 restraints weight = 9629.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.066894 restraints weight = 6865.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.067622 restraints weight = 5352.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10259  Z= 0.153
  Angle     :  0.573   8.262  13865  Z= 0.305
  Chirality :  0.041   0.181   1523
  Planarity :  0.003   0.044   1803
  Dihedral  :  4.858  21.134   1394
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.33 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.22), residues: 1273
  helix:  0.70 (0.26), residues: 405
  sheet: -1.26 (0.37), residues: 180
  loop : -2.29 (0.21), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 826 
 TYR   0.021   0.001   TYR A1197 
 PHE   0.023   0.002   PHE A1879 
 TRP   0.008   0.001   TRP A1405 
 HIS   0.003   0.001   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10259)
  covalent geometry    : angle       0.57324 (13865)
  hydrogen bonds       : bond        0.03545 (  311)
  hydrogen bonds       : angle       4.50239 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 66
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8637 (p90) cc_final: 0.7874 (p90)
REVERT: A 1171 ILE cc_start: 0.8767 (tp) cc_final: 0.8485 (pt)
REVERT: A 1241 TYR cc_start: 0.8747 (t80) cc_final: 0.8334 (t80)
REVERT: A 1594 LEU cc_start: 0.9240 (mp) cc_final: 0.8935 (mp)
REVERT: A 1605 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: A 1654 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7387 (p90)
REVERT: A 1679 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7429 (t0)
REVERT: A 1698 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7216 (tm-30)
REVERT: A 1800 MET cc_start: 0.8249 (tpp) cc_final: 0.7559 (tpp)
REVERT: A 1871 MET cc_start: 0.8234 (mtp) cc_final: 0.8022 (mtp)
  outliers start: 41
  outliers final: 32
  residues processed: 100
  average time/residue: 0.0911
  time to fit residues: 13.3701
Evaluate side-chains
  95 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 61
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  979 GLN
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1164 ASP
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1256 VAL
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Chi-restraints excluded: chain A residue 1947 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    0.1980
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A1198 GLN
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.075337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.063030 restraints weight = 29987.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.065292 restraints weight = 15129.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.066846 restraints weight = 9508.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.067909 restraints weight = 6789.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.068564 restraints weight = 5306.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10259  Z= 0.127
  Angle     :  0.560  10.334  13865  Z= 0.295
  Chirality :  0.041   0.160   1523
  Planarity :  0.003   0.044   1803
  Dihedral  :  4.658  19.938   1394
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.42 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.22), residues: 1273
  helix:  0.76 (0.26), residues: 409
  sheet: -1.18 (0.37), residues: 184
  loop : -2.26 (0.21), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1052 
 TYR   0.023   0.001   TYR A1197 
 PHE   0.022   0.001   PHE A1879 
 TRP   0.008   0.001   TRP A1405 
 HIS   0.003   0.000   HIS A1604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10259)
  covalent geometry    : angle       0.56023 (13865)
  hydrogen bonds       : bond        0.03350 (  311)
  hydrogen bonds       : angle       4.38372 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 67
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8560 (p90) cc_final: 0.7805 (p90)
REVERT: A 1241 TYR cc_start: 0.8723 (t80) cc_final: 0.8354 (t80)
REVERT: A 1444 THR cc_start: 0.9523 (p) cc_final: 0.9253 (p)
REVERT: A 1594 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8912 (mp)
REVERT: A 1605 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7816 (mm-30)
REVERT: A 1654 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7298 (p90)
REVERT: A 1679 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7281 (t0)
REVERT: A 1698 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7210 (tm-30)
REVERT: A 1800 MET cc_start: 0.8276 (tpp) cc_final: 0.7560 (tpp)
REVERT: A 1871 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7976 (mtp)
  outliers start: 41
  outliers final: 32
  residues processed: 99
  average time/residue: 0.0926
  time to fit residues: 13.4354
Evaluate side-chains
  97 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 61
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1256 VAL
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1871 MET
Chi-restraints excluded: chain A residue 1894 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 110 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 764 ASN
** A1391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.073699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.061635 restraints weight = 30516.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.063847 restraints weight = 15411.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.065355 restraints weight = 9634.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.066351 restraints weight = 6872.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.067077 restraints weight = 5396.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10259  Z= 0.193
  Angle     :  0.605  10.376  13865  Z= 0.317
  Chirality :  0.042   0.169   1523
  Planarity :  0.004   0.058   1803
  Dihedral  :  4.785  20.783   1394
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 16.88 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.22), residues: 1273
  helix:  0.69 (0.26), residues: 407
  sheet: -1.23 (0.38), residues: 180
  loop : -2.25 (0.21), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1225 
 TYR   0.021   0.001   TYR A1197 
 PHE   0.023   0.002   PHE A1879 
 TRP   0.007   0.001   TRP A1515 
 HIS   0.003   0.001   HIS A1608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (10259)
  covalent geometry    : angle       0.60530 (13865)
  hydrogen bonds       : bond        0.03552 (  311)
  hydrogen bonds       : angle       4.49498 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 59
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8642 (p90) cc_final: 0.7830 (p90)
REVERT: A 1241 TYR cc_start: 0.8752 (t80) cc_final: 0.8368 (t80)
REVERT: A 1444 THR cc_start: 0.9613 (p) cc_final: 0.9349 (p)
REVERT: A 1594 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8949 (mp)
REVERT: A 1605 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7839 (mm-30)
REVERT: A 1654 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7351 (p90)
REVERT: A 1679 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7340 (t0)
REVERT: A 1698 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7312 (tm-30)
REVERT: A 1800 MET cc_start: 0.8321 (tpp) cc_final: 0.7624 (tpp)
  outliers start: 42
  outliers final: 33
  residues processed: 93
  average time/residue: 0.1007
  time to fit residues: 13.6916
Evaluate side-chains
  91 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 55
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1256 VAL
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1332 ASP
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1679 ASP
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 110 optimal weight:    0.8980
   chunk 94 optimal weight:    0.0770
   chunk 23 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 126 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.9140

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

Flipped N/Q/H residues before XYZ refinement:
** A1391 HIS ** 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 = 0.3212 r_free = 0.3212 target = 0.074900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.062718 restraints weight = 29989.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.064964 restraints weight = 15263.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.066487 restraints weight = 9595.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.067537 restraints weight = 6869.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.068250 restraints weight = 5365.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10259  Z= 0.139
  Angle     :  0.582  10.593  13865  Z= 0.305
  Chirality :  0.041   0.161   1523
  Planarity :  0.003   0.061   1803
  Dihedral  :  4.660  20.189   1394
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 17.35 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.22), residues: 1273
  helix:  0.79 (0.26), residues: 402
  sheet: -1.04 (0.39), residues: 171
  loop : -2.24 (0.20), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1052 
 TYR   0.016   0.001   TYR A1197 
 PHE   0.023   0.001   PHE A1879 
 TRP   0.007   0.001   TRP A1405 
 HIS   0.006   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10259)
  covalent geometry    : angle       0.58169 (13865)
  hydrogen bonds       : bond        0.03390 (  311)
  hydrogen bonds       : angle       4.40327 (  927)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 64
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  977 HIS cc_start: 0.8588 (p90) cc_final: 0.7796 (p90)
REVERT: A 1241 TYR cc_start: 0.8735 (t80) cc_final: 0.8366 (t80)
REVERT: A 1444 THR cc_start: 0.9562 (p) cc_final: 0.9289 (p)
REVERT: A 1449 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8997 (ptpp)
REVERT: A 1594 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8905 (mp)
REVERT: A 1605 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7842 (mm-30)
REVERT: A 1654 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7293 (p90)
REVERT: A 1698 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7283 (tm-30)
REVERT: A 1800 MET cc_start: 0.8284 (tpp) cc_final: 0.7550 (tpp)
  outliers start: 38
  outliers final: 33
  residues processed: 96
  average time/residue: 0.0910
  time to fit residues: 12.7735
Evaluate side-chains
  94 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 58
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  824 THR
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue 1026 VAL
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1169 THR
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1256 VAL
Chi-restraints excluded: chain A residue 1272 GLN
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1294 VAL
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1332 ASP
Chi-restraints excluded: chain A residue 1383 THR
Chi-restraints excluded: chain A residue 1415 VAL
Chi-restraints excluded: chain A residue 1449 LYS
Chi-restraints excluded: chain A residue 1454 VAL
Chi-restraints excluded: chain A residue 1460 LEU
Chi-restraints excluded: chain A residue 1535 ASP
Chi-restraints excluded: chain A residue 1589 MET
Chi-restraints excluded: chain A residue 1594 LEU
Chi-restraints excluded: chain A residue 1648 ILE
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1701 SER
Chi-restraints excluded: chain A residue 1737 VAL
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1779 ILE
Chi-restraints excluded: chain A residue 1836 THR
Chi-restraints excluded: chain A residue 1894 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0370
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0870
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
** A1391 HIS ** 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 = 0.3233 r_free = 0.3233 target = 0.075958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.063832 restraints weight = 30195.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.066133 restraints weight = 15208.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.067677 restraints weight = 9475.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.068738 restraints weight = 6731.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.069468 restraints weight = 5230.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10259  Z= 0.113
  Angle     :  0.595  12.167  13865  Z= 0.306
  Chirality :  0.041   0.159   1523
  Planarity :  0.004   0.061   1803
  Dihedral  :  4.536  19.421   1394
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.90 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.22), residues: 1273
  helix:  0.75 (0.26), residues: 409
  sheet: -0.87 (0.39), residues: 165
  loop : -2.22 (0.21), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1673 
 TYR   0.015   0.001   TYR A1197 
 PHE   0.022   0.001   PHE A1879 
 TRP   0.008   0.001   TRP A1405 
 HIS   0.006   0.001   HIS A 937 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10259)
  covalent geometry    : angle       0.59453 (13865)
  hydrogen bonds       : bond        0.03343 (  311)
  hydrogen bonds       : angle       4.35826 (  927)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1439.57 seconds
wall clock time: 25 minutes 49.50 seconds (1549.50 seconds total)