Starting phenix.real_space_refine
on Thu Jul  2 20:19:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b13_44064/07_2026/9b13_44064.map"
  }
  resolution = 3.9
  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=   0.967
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      49      5.16       5
     C    6358      2.51       5
     N    1699      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10013
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6745
          Classifications: {'peptide': 842}
          Link IDs: {'PTRANS': 44, 'TRANS': 797}
          Chain breaks: 8
    Chain: "H"
      Number of atoms: 1697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1697
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 214}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1570
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 195}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 0
          Ad-hoc single atom residues: {' CA': 1}
          Chain breaks: 1
  Time building chain proxies: 2.14, per 1000 atoms: 0.21
  Number of scatterers: 10013
  At special positions: 0
  Unit cell: (96.481, 81.928, 170.863, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      49     16.00
     O    1906      8.00
     N    1699      7.00
     C    6358      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 160 " - pdb=" SG  CYS H 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 359.9 milliseconds
  

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2406

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 18 sheets defined
      27.3% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 844 through 848
    Processing helix  chain 'A' and resid 851 through 861
    Processing helix  chain 'A' and resid 934 through 936
      No H-bonds generated for 'chain 'A' and resid 934 through 936'
    Processing helix  chain 'A' and resid 949 through 958
    Processing helix  chain 'A' and resid 963 through 966
    Processing helix  chain 'A' and resid 988 through 1010
      removed outlier: 3.927A  pdb=" N   GLU A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1028
    Processing helix  chain 'A' and resid 1038 through 1046
    Processing helix  chain 'A' and resid 1195 through 1208
    Processing helix  chain 'A' and resid 1211 through 1219
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1274 through 1288
    Processing helix  chain 'A' and resid 1308 through 1317
    Processing helix  chain 'A' and resid 1323 through 1335
      removed outlier: 3.623A  pdb=" N   LYS A1333 " --> pdb=" O   SER A1329 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   PHE A1334 " --> pdb=" O   ILE A1330 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A1335 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1337 through 1343
      removed outlier: 3.546A  pdb=" N   CYS A1341 " --> pdb=" O   ASN A1337 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   HIS A1342 " --> pdb=" O   ILE A1338 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLN A1343 " --> pdb=" O   SER A1339 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1337 through 1343'
    Processing helix  chain 'A' and resid 1347 through 1356
    Processing helix  chain 'A' and resid 1404 through 1412
      removed outlier: 3.914A  pdb=" N   GLN A1408 " --> pdb=" O   GLU A1404 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A1410 " --> pdb=" O   TYR A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1443 through 1453
      removed outlier: 3.781A  pdb=" N   SER A1453 " --> pdb=" O   ALA A1449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1471 through 1486
    Processing helix  chain 'A' and resid 1496 through 1500
    Processing helix  chain 'A' and resid 1509 through 1513
    Processing helix  chain 'A' and resid 1643 through 1648
    Processing helix  chain 'A' and resid 1731 through 1735
    Processing helix  chain 'A' and resid 1741 through 1751
    Processing helix  chain 'A' and resid 1752 through 1759
    Processing helix  chain 'A' and resid 1780 through 1787
      removed outlier: 4.412A  pdb=" N   HIS A1786 " --> pdb=" O   MET A1782 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A1787 " --> pdb=" O   PHE A1783 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1799 through 1809
      removed outlier: 3.701A  pdb=" N   PHE A1809 " --> pdb=" O   ASN A1805 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1810 through 1815
      removed outlier: 3.790A  pdb=" N   GLY A1813 " --> pdb=" O   GLU A1810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1821 through 1826
      removed outlier: 4.079A  pdb=" N   TRP A1825 " --> pdb=" O   PRO A1821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1909 through 1912
      removed outlier: 3.778A  pdb=" N   LEU A1912 " --> pdb=" O   PHE A1909 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1909 through 1912'
    Processing helix  chain 'A' and resid 1936 through 1938
      No H-bonds generated for 'chain 'A' and resid 1936 through 1938'
    Processing helix  chain 'A' and resid 1977 through 1983
      removed outlier: 3.524A  pdb=" N   ASN A1983 " --> pdb=" O   SER A1979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1984 through 1991
      removed outlier: 4.691A  pdb=" N   LYS A1988 " --> pdb=" O   THR A1984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2016 through 2026
    Processing helix  chain 'A' and resid 2068 through 2075
      removed outlier: 3.801A  pdb=" N   ILE A2072 " --> pdb=" O   ASP A2068 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 31 through 35
    Processing helix  chain 'H' and resid 90 through 94
    Processing helix  chain 'H' and resid 176 through 178
      No H-bonds generated for 'chain 'H' and resid 176 through 178'
    Processing helix  chain 'H' and resid 207 through 209
      No H-bonds generated for 'chain 'H' and resid 207 through 209'
    Processing helix  chain 'H' and resid 221 through 224
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.500A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 122 through 128
      removed outlier: 3.739A  pdb=" N   SER L 128 " --> pdb=" O   SER L 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 873 through 879
      removed outlier: 3.599A  pdb=" N   ALA A 862 " --> pdb=" O   LEU A 879 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   HIS A 984 " --> pdb=" O   TYR A 867 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ALA A 940 " --> pdb=" O   LEU A 972 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1223 through 1225
      removed outlier: 3.500A  pdb=" N   CYS A1225 " --> pdb=" O   ILE A1302 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE A1302 " --> pdb=" O   CYS A1225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1441 through 1442
      removed outlier: 6.481A  pdb=" N   ILE A1417 " --> pdb=" O   SER A1465 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   GLU A1467 " --> pdb=" O   ILE A1417 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU A1419 " --> pdb=" O   GLU A1467 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   HIS A1469 " --> pdb=" O   LEU A1419 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   CYS A1421 " --> pdb=" O   HIS A1469 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ILE A1462 " --> pdb=" O   LEU A1517 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   LYS A1519 " --> pdb=" O   ILE A1462 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   ILE A1464 " --> pdb=" O   LYS A1519 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   CYS A1653 " --> pdb=" O   LEU A1518 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1737 through 1740
      removed outlier: 7.162A  pdb=" N   SER A1737 " --> pdb=" O   ARG A1765 " (cutoff:3.500A)
      removed outlier: 8.738A  pdb=" N   TYR A1767 " --> pdb=" O   SER A1737 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LEU A1739 " --> pdb=" O   TYR A1767 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1901 through 1907
      removed outlier: 4.951A  pdb=" N   TYR A1850 " --> pdb=" O   MET A1967 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   MET A1967 " --> pdb=" O   TYR A1850 " (cutoff:3.500A)
      removed outlier: 5.329A  pdb=" N   LEU A1852 " --> pdb=" O   ARG A1965 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   ARG A1965 " --> pdb=" O   LEU A1852 " (cutoff:3.500A)
      removed outlier: 5.306A  pdb=" N   ILE A1854 " --> pdb=" O   ASN A1963 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ASN A1963 " --> pdb=" O   ILE A1854 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   SER A1958 " --> pdb=" O   LEU A1947 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A1947 " --> pdb=" O   SER A1958 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A1964 " --> pdb=" O   GLY A1941 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1869 through 1872
      removed outlier: 3.825A  pdb=" N   ASP A1874 " --> pdb=" O   ARG A1916 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   CYS A1883 " --> pdb=" O   VAL A1875 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1869 through 1872
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2006 through 2011
      removed outlier: 3.716A  pdb=" N   VAL A1997 " --> pdb=" O   ALA A2007 " (cutoff:3.500A)
      removed outlier: 18.326A  pdb=" N   LYS A1994 " --> pdb=" O   TYR A2082 " (cutoff:3.500A)
      removed outlier: 12.575A  pdb=" N   GLY A2084 " --> pdb=" O   LYS A1994 " (cutoff:3.500A)
      removed outlier: 8.388A  pdb=" N   THR A1996 " --> pdb=" O   GLY A2084 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ILE A2086 " --> pdb=" O   THR A1996 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A2088 " --> pdb=" O   HIS A1998 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A2083 " --> pdb=" O   HIS A2045 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS A2045 " --> pdb=" O   VAL A2083 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL A2087 " --> pdb=" O   MET A2041 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 7 through 10
      removed outlier: 3.693A  pdb=" N   CYS H  25 " --> pdb=" O   ALA H  82 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA H  82 " --> pdb=" O   CYS H  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 49 through 54
      removed outlier: 6.775A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER H  36 " --> pdb=" O   SER H 102 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 49 through 54
      removed outlier: 6.775A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 144
      removed outlier: 3.613A  pdb=" N   GLY H 159 " --> pdb=" O   LEU H 144 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   TYR H 196 " --> pdb=" O   ASP H 164 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 171 through 174
      removed outlier: 4.360A  pdb=" N   TYR H 214 " --> pdb=" O   VAL H 231 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.667A  pdb=" N   ALA L  85 " --> pdb=" O   VAL L 105 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 20 through 25
    Processing sheet with id=AB7, first strand: chain 'L' and resid 90 through 92
      removed outlier: 3.693A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 115 through 119
      removed outlier: 5.349A  pdb=" N   SER L 132 " --> pdb=" O   LEU L 182 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU L 182 " --> pdb=" O   SER L 132 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   VAL L 134 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU L 180 " --> pdb=" O   VAL L 134 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   LEU L 136 " --> pdb=" O   SER L 178 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   SER L 178 " --> pdb=" O   LEU L 136 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   ASN L 138 " --> pdb=" O   LEU L 176 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU L 176 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 154 through 156
      removed outlier: 4.266A  pdb=" N   TRP L 149 " --> pdb=" O   GLN L 156 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    897 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.31 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: 3237
        1.34 -     1.46: 2369
        1.46 -     1.58: 4561
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 10237
  Sorted by residual:
  bond pdb=" N   HIS A 838 "
       pdb=" CA  HIS A 838 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   GLU H   4 "
       pdb=" CA  GLU H   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   ILE L   3 "
       pdb=" CA  ILE L   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.72e+00
  bond pdb=" CA  ILE A1854 "
       pdb=" C   ILE A1854 "
    ideal  model  delta    sigma   weight residual
    1.527  1.515  0.012 9.70e-03 1.06e+04 1.55e+00
  bond pdb=" CB  PRO A2090 "
       pdb=" CG  PRO A2090 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 5.00e-02 4.00e+02 1.01e+00
  ... (remaining 10232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 13171
        1.14 -     2.28: 584
        2.28 -     3.42: 89
        3.42 -     4.56: 27
        4.56 -     5.70: 3
  Bond angle restraints: 13874
  Sorted by residual:
  angle pdb=" C   SER L  53 "
        pdb=" CA  SER L  53 "
        pdb=" CB  SER L  53 "
      ideal   model   delta    sigma   weight residual
     115.79  110.42    5.37 1.19e+00 7.06e-01 2.04e+01
  angle pdb=" C   SER L  51 "
        pdb=" CA  SER L  51 "
        pdb=" CB  SER L  51 "
      ideal   model   delta    sigma   weight residual
     117.23  111.53    5.70 1.36e+00 5.41e-01 1.76e+01
  angle pdb=" CA  SER L  51 "
        pdb=" C   SER L  51 "
        pdb=" N   ALA L  52 "
      ideal   model   delta    sigma   weight residual
     119.98  117.66    2.32 8.50e-01 1.38e+00 7.42e+00
  angle pdb=" N   GLU A2079 "
        pdb=" CA  GLU A2079 "
        pdb=" C   GLU A2079 "
      ideal   model   delta    sigma   weight residual
     114.56  111.27    3.29 1.27e+00 6.20e-01 6.73e+00
  angle pdb=" CA  TYR A2082 "
        pdb=" CB  TYR A2082 "
        pdb=" CG  TYR A2082 "
      ideal   model   delta    sigma   weight residual
     113.90  118.25   -4.35 1.80e+00 3.09e-01 5.84e+00
  ... (remaining 13869 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.22: 5742
       16.22 -    32.45: 335
       32.45 -    48.67: 65
       48.67 -    64.90: 19
       64.90 -    81.12: 2
  Dihedral angle restraints: 6163
    sinusoidal: 2449
      harmonic: 3714
  Sorted by residual:
  dihedral pdb=" CA  LYS A1333 "
           pdb=" C   LYS A1333 "
           pdb=" N   PHE A1334 "
           pdb=" CA  PHE A1334 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.39  -20.61     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO A1971 "
           pdb=" C   PRO A1971 "
           pdb=" N   SER A1972 "
           pdb=" CA  SER A1972 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.29  -19.71     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  LEU A 842 "
           pdb=" C   LEU A 842 "
           pdb=" N   ILE A 843 "
           pdb=" CA  ILE A 843 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 6160 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 962
       0.031 -    0.062: 422
       0.062 -    0.094: 80
       0.094 -    0.125: 84
       0.125 -    0.156: 8
  Chirality restraints: 1556
  Sorted by residual:
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.08e-01
  chirality pdb=" CA  ILE A1927 "
            pdb=" N   ILE A1927 "
            pdb=" C   ILE A1927 "
            pdb=" CB  ILE A1927 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  ILE L   3 "
            pdb=" N   ILE L   3 "
            pdb=" C   ILE L   3 "
            pdb=" CB  ILE L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 1553 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A2077 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.69e+00
        pdb=" N   PRO A2078 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A2078 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A2078 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1658 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A1659 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A1659 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1659 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A1506 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.60e+00
        pdb=" N   PRO A1507 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A1507 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1507 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 218
        2.63 -     3.20: 9671
        3.20 -     3.77: 14485
        3.77 -     4.33: 20637
        4.33 -     4.90: 33476
  Nonbonded interactions: 78487
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 963 "
            pdb=" OG1 THR A 967 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" OD1 ASN A2012 "
            pdb=" OG1 THR A2015 "
     model   vdw
     2.082 3.040
  nonbonded pdb=" O   TYR L 187 "
            pdb=" OH  TYR L 193 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OD1 ASN A1316 "
            pdb=" N   GLY A2084 "
     model   vdw
     2.101 3.120
  nonbonded pdb=" NZ  LYS H 226 "
            pdb=" OD1 ASP H 228 "
     model   vdw
     2.102 3.120
  ... (remaining 78482 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             15.140
  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:          0.370
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.850
  Find NCS groups from input model:        0.050
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10241  Z= 0.199
  Angle     :  0.570   5.698  13882  Z= 0.321
  Chirality :  0.041   0.156   1556
  Planarity :  0.004   0.048   1774
  Dihedral  : 11.167  81.123   3745
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.43 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  :  5.49 %
    Favored  : 90.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    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: -1.29 (0.24), residues: 1246
  helix: -0.05 (0.32), residues: 254
  sheet: -0.73 (0.29), residues: 340
  loop : -1.22 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1452 
 TYR   0.015   0.001   TYR H 104 
 PHE   0.012   0.001   PHE A1218 
 TRP   0.007   0.001   TRP A 890 
 HIS   0.003   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.20 (10237)
  covalent geometry    : angle       0.57049 /  0.32 (13874)
  SS BOND              : bond        0.00346 /  0.18 (    4)
  SS BOND              : angle       0.50325 /  0.35 (    8)
  hydrogen bonds       : bond        0.22921 / 15.53 (  342)
  hydrogen bonds       : angle       8.85516 /  6.21 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 251
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7663 (mt) cc_final: 0.7266 (tt)
REVERT: A 1754 LYS cc_start: 0.8258 (mttt) cc_final: 0.7976 (tttt)
REVERT: A 1767 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7867 (p90)
REVERT: A 1773 ILE cc_start: 0.8289 (pt) cc_final: 0.8012 (mm)
REVERT: A 1826 ASP cc_start: 0.6894 (t0) cc_final: 0.6591 (t0)
REVERT: A 1895 LEU cc_start: 0.8590 (mt) cc_final: 0.8335 (mp)
REVERT: A 1981 MET cc_start: 0.8611 (mmm) cc_final: 0.8407 (mmt)
REVERT: A 2038 TYR cc_start: 0.7857 (m-80) cc_final: 0.7610 (m-80)
REVERT: H   89 LEU cc_start: 0.8742 (mt) cc_final: 0.7877 (mt)
REVERT: L   91 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8146 (pp30)
REVERT: L  140 PHE cc_start: 0.8373 (p90) cc_final: 0.7739 (p90)
REVERT: L  174 TYR cc_start: 0.7439 (m-80) cc_final: 0.7203 (m-80)
  outliers start: 42
  outliers final: 20
  residues processed: 285
  average time/residue: 0.1186
  time to fit residues: 45.8671
Evaluate side-chains
  196 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1767 TYR
Chi-restraints excluded: chain A residue 1774 ASP
Chi-restraints excluded: chain A residue 1812 ASN
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   99 CYS
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain L residue   54 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.1980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 856 GLN
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** A1408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1762 GLN
A1777 ASN
A1812 ASN
A1902 GLN
** A1993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.158147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.122691 restraints weight = 19508.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122328 restraints weight = 13445.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123459 restraints weight = 11280.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.124348 restraints weight = 8838.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.124529 restraints weight = 8017.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10241  Z= 0.133
  Angle     :  0.634   8.928  13882  Z= 0.328
  Chirality :  0.045   0.236   1556
  Planarity :  0.004   0.045   1774
  Dihedral  :  6.913  59.742   1399
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.06 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 10.63 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.24), residues: 1246
  helix:  0.88 (0.32), residues: 272
  sheet: -0.43 (0.28), residues: 359
  loop : -0.95 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 101 
 TYR   0.015   0.002   TYR A 942 
 PHE   0.017   0.002   PHE A1206 
 TRP   0.007   0.001   TRP A 845 
 HIS   0.007   0.001   HIS A 951 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (10237)
  covalent geometry    : angle       0.63355 /  0.33 (13874)
  SS BOND              : bond        0.00507 /  0.25 (    4)
  SS BOND              : angle       0.99164 /  0.74 (    8)
  hydrogen bonds       : bond        0.03952 /  2.64 (  342)
  hydrogen bonds       : angle       5.99097 /  4.26 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 208
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7666 (mt) cc_final: 0.7280 (tt)
REVERT: A 1278 GLN cc_start: 0.8705 (mp10) cc_final: 0.8076 (mp10)
REVERT: A 1373 LYS cc_start: 0.9124 (pttt) cc_final: 0.8855 (pttp)
REVERT: A 1404 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: A 1826 ASP cc_start: 0.6948 (t0) cc_final: 0.6561 (t0)
REVERT: A 1888 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7230 (tttm)
REVERT: A 1933 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8251 (pt)
REVERT: A 2038 TYR cc_start: 0.7679 (m-80) cc_final: 0.7403 (m-10)
REVERT: H   94 THR cc_start: 0.8048 (m) cc_final: 0.7743 (p)
REVERT: L   83 ASP cc_start: 0.7936 (m-30) cc_final: 0.7684 (m-30)
REVERT: L   91 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7833 (tm-30)
REVERT: L  140 PHE cc_start: 0.8199 (p90) cc_final: 0.7764 (p90)
REVERT: L  141 TYR cc_start: 0.7455 (t80) cc_final: 0.7211 (t80)
  outliers start: 42
  outliers final: 29
  residues processed: 232
  average time/residue: 0.1046
  time to fit residues: 33.4070
Evaluate side-chains
  201 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 169
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1888 LYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  142 PHE
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  130 THR
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   chunk 120 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
A1408 GLN
H 175 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 200 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.155410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.120347 restraints weight = 19940.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.118266 restraints weight = 13347.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.119839 restraints weight = 11289.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.120143 restraints weight = 9070.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.120462 restraints weight = 8360.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10241  Z= 0.159
  Angle     :  0.634   8.036  13882  Z= 0.324
  Chirality :  0.044   0.179   1556
  Planarity :  0.004   0.043   1774
  Dihedral  :  6.737  58.922   1386
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 12.05 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.25), residues: 1246
  helix:  0.85 (0.31), residues: 272
  sheet: -0.36 (0.28), residues: 370
  loop : -0.89 (0.27), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  70 
 TYR   0.015   0.001   TYR H 104 
 PHE   0.015   0.001   PHE A 857 
 TRP   0.009   0.001   TRP H 123 
 HIS   0.006   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 (10237)
  covalent geometry    : angle       0.63372 /  0.32 (13874)
  SS BOND              : bond        0.00471 /  0.24 (    4)
  SS BOND              : angle       0.63092 /  0.50 (    8)
  hydrogen bonds       : bond        0.03676 /  2.45 (  342)
  hydrogen bonds       : angle       5.68041 /  4.03 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 176
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  995 LEU cc_start: 0.7719 (mt) cc_final: 0.7401 (tt)
REVERT: A 1373 LYS cc_start: 0.9170 (pttt) cc_final: 0.8933 (pttm)
REVERT: A 1826 ASP cc_start: 0.7138 (t0) cc_final: 0.6727 (t0)
REVERT: A 1933 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8335 (pt)
REVERT: A 2041 MET cc_start: 0.7732 (tmm) cc_final: 0.7238 (tmm)
REVERT: L   91 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7797 (tm-30)
REVERT: L  140 PHE cc_start: 0.8264 (p90) cc_final: 0.7854 (p90)
REVERT: L  141 TYR cc_start: 0.7613 (t80) cc_final: 0.7304 (t80)
REVERT: L  174 TYR cc_start: 0.7255 (m-80) cc_final: 0.6946 (m-80)
  outliers start: 50
  outliers final: 38
  residues processed: 206
  average time/residue: 0.1030
  time to fit residues: 28.6706
Evaluate side-chains
  196 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 156
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1519 LYS
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1797 THR
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  130 THR
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 113 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 117 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
A1991 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.155604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.119415 restraints weight = 20012.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.121526 restraints weight = 13593.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122512 restraints weight = 8990.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.123402 restraints weight = 7855.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.123556 restraints weight = 7311.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10241  Z= 0.152
  Angle     :  0.617   8.208  13882  Z= 0.316
  Chirality :  0.044   0.179   1556
  Planarity :  0.004   0.043   1774
  Dihedral  :  6.611  58.460   1386
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.54 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 13.82 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.24), residues: 1246
  helix:  0.85 (0.31), residues: 265
  sheet: -0.43 (0.27), residues: 379
  loop : -0.91 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A2055 
 TYR   0.014   0.001   TYR H 104 
 PHE   0.016   0.001   PHE A 857 
 TRP   0.008   0.001   TRP H 123 
 HIS   0.005   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00354 /  0.15 (10237)
  covalent geometry    : angle       0.61701 /  0.32 (13874)
  SS BOND              : bond        0.00340 /  0.17 (    4)
  SS BOND              : angle       0.52461 /  0.40 (    8)
  hydrogen bonds       : bond        0.03479 /  2.33 (  342)
  hydrogen bonds       : angle       5.48460 /  3.89 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 161
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1315 VAL cc_start: 0.8601 (p) cc_final: 0.8400 (p)
REVERT: A 1373 LYS cc_start: 0.9154 (pttt) cc_final: 0.8887 (pttm)
REVERT: A 1404 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A 1745 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7068 (mtpt)
REVERT: A 1826 ASP cc_start: 0.7015 (t0) cc_final: 0.6647 (t0)
REVERT: A 1933 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8316 (pt)
REVERT: A 2041 MET cc_start: 0.7686 (tmm) cc_final: 0.7237 (tmm)
REVERT: H   49 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6104 (mm-30)
REVERT: L   91 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8082 (pp30)
REVERT: L  174 TYR cc_start: 0.7117 (m-80) cc_final: 0.6864 (m-80)
  outliers start: 54
  outliers final: 44
  residues processed: 195
  average time/residue: 0.1030
  time to fit residues: 27.8431
Evaluate side-chains
  195 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1225 CYS
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1328 LEU
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1745 LYS
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 1933 ILE
Chi-restraints excluded: chain A residue 1944 HIS
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  164 ASP
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  105 VAL
Chi-restraints excluded: chain L residue  130 THR
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 105 optimal weight:    8.9990
   chunk 43 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 116 optimal weight:   40.0000
   overall best weight:    2.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.153817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.118643 restraints weight = 20210.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.117100 restraints weight = 13999.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.118697 restraints weight = 11636.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.118899 restraints weight = 9528.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119246 restraints weight = 8919.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10241  Z= 0.191
  Angle     :  0.653   8.705  13882  Z= 0.332
  Chirality :  0.044   0.186   1556
  Planarity :  0.004   0.053   1774
  Dihedral  :  6.684  59.455   1386
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.10 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 14.79 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.24), residues: 1246
  helix:  0.55 (0.31), residues: 265
  sheet: -0.42 (0.28), residues: 359
  loop : -1.04 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A2055 
 TYR   0.026   0.002   TYR H 108 
 PHE   0.015   0.002   PHE A 857 
 TRP   0.010   0.002   TRP H 123 
 HIS   0.005   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00445 /  0.19 (10237)
  covalent geometry    : angle       0.65272 /  0.33 (13874)
  SS BOND              : bond        0.00374 /  0.19 (    4)
  SS BOND              : angle       0.62747 /  0.49 (    8)
  hydrogen bonds       : bond        0.03623 /  2.44 (  342)
  hydrogen bonds       : angle       5.60151 /  3.95 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 153
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1027 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8070 (t80)
REVERT: A 1373 LYS cc_start: 0.9183 (pttt) cc_final: 0.8954 (pttm)
REVERT: A 1745 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7083 (mtpt)
REVERT: A 1826 ASP cc_start: 0.7188 (t0) cc_final: 0.6776 (t0)
REVERT: A 2041 MET cc_start: 0.7781 (tmm) cc_final: 0.7217 (tmm)
REVERT: L   91 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8195 (pp30)
  outliers start: 58
  outliers final: 44
  residues processed: 191
  average time/residue: 0.0967
  time to fit residues: 25.7949
Evaluate side-chains
  194 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 147
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  984 HIS
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1745 LYS
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  190 LEU
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   91 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   chunk 94 optimal weight:    1.9990
   chunk 117 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1902 GLN
A1993 HIS
H  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.156131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.121324 restraints weight = 20116.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.120034 restraints weight = 13617.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121572 restraints weight = 10594.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.121978 restraints weight = 8328.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.122118 restraints weight = 7816.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10241  Z= 0.136
  Angle     :  0.618   8.683  13882  Z= 0.313
  Chirality :  0.044   0.219   1556
  Planarity :  0.004   0.051   1774
  Dihedral  :  6.109  59.899   1382
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.22 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 16.47 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.24), residues: 1246
  helix:  0.60 (0.31), residues: 265
  sheet: -0.27 (0.28), residues: 354
  loop : -0.98 (0.26), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A2055 
 TYR   0.020   0.001   TYR H 108 
 PHE   0.011   0.001   PHE A1199 
 TRP   0.006   0.001   TRP A1422 
 HIS   0.005   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 (10237)
  covalent geometry    : angle       0.61825 /  0.31 (13874)
  SS BOND              : bond        0.00286 /  0.14 (    4)
  SS BOND              : angle       0.55367 /  0.39 (    8)
  hydrogen bonds       : bond        0.03380 /  2.30 (  342)
  hydrogen bonds       : angle       5.33688 /  3.77 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 163
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7957 (pt0)
REVERT: A 1027 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.8008 (t80)
REVERT: A 1373 LYS cc_start: 0.9204 (pttt) cc_final: 0.8895 (pttp)
REVERT: A 1400 GLU cc_start: 0.8411 (mp0) cc_final: 0.8097 (mp0)
REVERT: A 1422 TRP cc_start: 0.8210 (m100) cc_final: 0.7965 (m100)
REVERT: A 1654 GLN cc_start: 0.8288 (mp10) cc_final: 0.7843 (mp10)
REVERT: A 1826 ASP cc_start: 0.7227 (t0) cc_final: 0.6806 (t0)
REVERT: A 1831 MET cc_start: 0.7042 (tpp) cc_final: 0.6836 (tpp)
REVERT: A 1845 MET cc_start: 0.5183 (mtt) cc_final: 0.4826 (mtt)
REVERT: A 2041 MET cc_start: 0.7710 (tmm) cc_final: 0.7286 (tmm)
REVERT: L   90 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7881 (pp30)
  outliers start: 48
  outliers final: 37
  residues processed: 192
  average time/residue: 0.1066
  time to fit residues: 28.1454
Evaluate side-chains
  182 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  969 VAL
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  190 LEU
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 103 optimal weight:    0.6980
   chunk 105 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 123 optimal weight:    8.9990
   chunk 41 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    1.4982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 951 HIS
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.155097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.120282 restraints weight = 20043.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.119469 restraints weight = 14085.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.120853 restraints weight = 12065.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.120938 restraints weight = 9373.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.121809 restraints weight = 8763.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  10241  Z= 0.158
  Angle     :  0.647   9.143  13882  Z= 0.325
  Chirality :  0.044   0.209   1556
  Planarity :  0.004   0.055   1774
  Dihedral  :  5.772  59.179   1376
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.70 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 16.65 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.24), residues: 1246
  helix:  0.56 (0.31), residues: 265
  sheet: -0.29 (0.28), residues: 347
  loop : -1.06 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  22 
 TYR   0.021   0.001   TYR H 108 
 PHE   0.013   0.001   PHE H  32 
 TRP   0.008   0.001   TRP A 890 
 HIS   0.005   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.16 (10237)
  covalent geometry    : angle       0.64728 /  0.32 (13874)
  SS BOND              : bond        0.00310 /  0.16 (    4)
  SS BOND              : angle       0.56737 /  0.39 (    8)
  hydrogen bonds       : bond        0.03386 /  2.30 (  342)
  hydrogen bonds       : angle       5.36577 /  3.79 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 154
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7932 (pt0)
REVERT: A 1027 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7974 (t80)
REVERT: A 1373 LYS cc_start: 0.9189 (pttt) cc_final: 0.8944 (pttm)
REVERT: A 1400 GLU cc_start: 0.8409 (mp0) cc_final: 0.8093 (mp0)
REVERT: A 1478 MET cc_start: 0.8580 (tpp) cc_final: 0.7621 (tpp)
REVERT: A 1654 GLN cc_start: 0.8316 (mp10) cc_final: 0.7897 (mp10)
REVERT: A 1826 ASP cc_start: 0.7131 (t0) cc_final: 0.6734 (t0)
REVERT: A 1831 MET cc_start: 0.7135 (tpp) cc_final: 0.6876 (tpp)
REVERT: A 1845 MET cc_start: 0.5249 (mtt) cc_final: 0.5004 (mtt)
REVERT: A 2041 MET cc_start: 0.7671 (tmm) cc_final: 0.7137 (tmm)
REVERT: H   22 ARG cc_start: 0.7053 (ttm110) cc_final: 0.6733 (ttm110)
REVERT: L   90 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7864 (pp30)
REVERT: L  184 LYS cc_start: 0.9346 (tppt) cc_final: 0.8948 (mmmm)
  outliers start: 51
  outliers final: 44
  residues processed: 187
  average time/residue: 0.1042
  time to fit residues: 27.0137
Evaluate side-chains
  193 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 146
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  951 HIS
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1490 LEU
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2021 LEU
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   37 ILE
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   22 ILE
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 116 optimal weight:   40.0000
   chunk 79 optimal weight:    0.0970
   chunk 49 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 115 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.154196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.118184 restraints weight = 20042.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.119712 restraints weight = 13066.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.120604 restraints weight = 9672.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121036 restraints weight = 8143.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.122043 restraints weight = 7697.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10241  Z= 0.180
  Angle     :  0.674   9.926  13882  Z= 0.337
  Chirality :  0.045   0.257   1556
  Planarity :  0.005   0.059   1774
  Dihedral  :  5.900  58.411   1376
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.42 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 17.36 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.24), residues: 1246
  helix:  0.39 (0.31), residues: 265
  sheet: -0.29 (0.28), residues: 344
  loop : -1.07 (0.25), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H  22 
 TYR   0.022   0.002   TYR H 108 
 PHE   0.015   0.001   PHE H  32 
 TRP   0.009   0.001   TRP A 890 
 HIS   0.010   0.001   HIS A 951 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00424 /  0.18 (10237)
  covalent geometry    : angle       0.67389 /  0.34 (13874)
  SS BOND              : bond        0.00314 /  0.16 (    4)
  SS BOND              : angle       0.56030 /  0.40 (    8)
  hydrogen bonds       : bond        0.03468 /  2.35 (  342)
  hydrogen bonds       : angle       5.49066 /  3.87 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 154
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7888 (pt0)
REVERT: A 1027 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7993 (t80)
REVERT: A 1373 LYS cc_start: 0.9207 (pttt) cc_final: 0.8948 (pttm)
REVERT: A 1400 GLU cc_start: 0.8372 (mp0) cc_final: 0.8055 (mp0)
REVERT: A 1654 GLN cc_start: 0.8370 (mp10) cc_final: 0.7930 (mp10)
REVERT: A 1826 ASP cc_start: 0.7176 (t0) cc_final: 0.6776 (t0)
REVERT: A 1845 MET cc_start: 0.5575 (mtt) cc_final: 0.5286 (mtt)
REVERT: A 2041 MET cc_start: 0.7774 (tmm) cc_final: 0.7185 (tmm)
REVERT: H  104 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (m-80)
REVERT: L   90 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7853 (pp30)
  outliers start: 53
  outliers final: 42
  residues processed: 187
  average time/residue: 0.0985
  time to fit residues: 25.8459
Evaluate side-chains
  189 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 143
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1785 LEU
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2021 LEU
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  104 TYR
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1758 HIS
H 191 GLN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.156609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.121471 restraints weight = 19873.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.121065 restraints weight = 13629.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122117 restraints weight = 11277.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.122310 restraints weight = 8946.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122637 restraints weight = 8083.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10241  Z= 0.128
  Angle     :  0.664  11.951  13882  Z= 0.327
  Chirality :  0.045   0.282   1556
  Planarity :  0.004   0.059   1774
  Dihedral  :  5.625  58.316   1376
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.90 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.07 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.24), residues: 1246
  helix:  0.59 (0.32), residues: 265
  sheet: -0.18 (0.28), residues: 348
  loop : -0.99 (0.25), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG H  22 
 TYR   0.016   0.001   TYR H 108 
 PHE   0.010   0.001   PHE A1199 
 TRP   0.006   0.001   TRP H 113 
 HIS   0.005   0.001   HIS A 951 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (10237)
  covalent geometry    : angle       0.66438 /  0.33 (13874)
  SS BOND              : bond        0.00282 /  0.14 (    4)
  SS BOND              : angle       0.58157 /  0.41 (    8)
  hydrogen bonds       : bond        0.03255 /  2.20 (  342)
  hydrogen bonds       : angle       5.23434 /  3.70 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 151
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7905 (pt0)
REVERT: A 1027 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.8001 (t80)
REVERT: A 1373 LYS cc_start: 0.9212 (pttt) cc_final: 0.8942 (pttm)
REVERT: A 1400 GLU cc_start: 0.8382 (mp0) cc_final: 0.8042 (mp0)
REVERT: A 1654 GLN cc_start: 0.8348 (mp10) cc_final: 0.7920 (mp10)
REVERT: A 1826 ASP cc_start: 0.7285 (t0) cc_final: 0.6820 (t0)
REVERT: A 1831 MET cc_start: 0.7066 (tpp) cc_final: 0.6706 (tpp)
REVERT: A 2041 MET cc_start: 0.7743 (tmm) cc_final: 0.7312 (tmm)
REVERT: L   90 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7939 (pp30)
REVERT: L  184 LYS cc_start: 0.9330 (tppt) cc_final: 0.8912 (mmmm)
  outliers start: 45
  outliers final: 37
  residues processed: 180
  average time/residue: 0.0904
  time to fit residues: 22.9845
Evaluate side-chains
  190 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 150
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2021 LEU
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 112 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1902 GLN
H  31 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.156021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.121426 restraints weight = 20025.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120643 restraints weight = 13580.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.122016 restraints weight = 11063.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.122375 restraints weight = 8939.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.122628 restraints weight = 8217.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10241  Z= 0.155
  Angle     :  0.684  11.125  13882  Z= 0.338
  Chirality :  0.046   0.290   1556
  Planarity :  0.005   0.059   1774
  Dihedral  :  5.612  57.706   1374
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.54 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 18.87 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.24), residues: 1246
  helix:  0.62 (0.32), residues: 265
  sheet: -0.12 (0.29), residues: 338
  loop : -0.95 (0.25), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG H  22 
 TYR   0.019   0.001   TYR H 108 
 PHE   0.017   0.001   PHE H  32 
 TRP   0.007   0.001   TRP H 123 
 HIS   0.005   0.001   HIS A1803 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.15 (10237)
  covalent geometry    : angle       0.68429 /  0.34 (13874)
  SS BOND              : bond        0.00254 /  0.13 (    4)
  SS BOND              : angle       0.55107 /  0.39 (    8)
  hydrogen bonds       : bond        0.03336 /  2.26 (  342)
  hydrogen bonds       : angle       5.28850 /  3.74 (  897)

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

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

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2492 Ramachandran restraints generated.
    1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 154
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  841 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (pt0)
REVERT: A 1027 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7936 (t80)
REVERT: A 1373 LYS cc_start: 0.9197 (pttt) cc_final: 0.8935 (pttm)
REVERT: A 1400 GLU cc_start: 0.8377 (mp0) cc_final: 0.8043 (mp0)
REVERT: A 1654 GLN cc_start: 0.8416 (mp10) cc_final: 0.8084 (mp10)
REVERT: A 1826 ASP cc_start: 0.7199 (t0) cc_final: 0.6782 (t0)
REVERT: A 1831 MET cc_start: 0.6925 (tpp) cc_final: 0.6561 (tpp)
REVERT: A 2041 MET cc_start: 0.7723 (tmm) cc_final: 0.7178 (tmm)
REVERT: L   90 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8018 (pp30)
REVERT: L  184 LYS cc_start: 0.9282 (tppt) cc_final: 0.9018 (mmmt)
  outliers start: 46
  outliers final: 40
  residues processed: 185
  average time/residue: 0.0910
  time to fit residues: 23.7675
Evaluate side-chains
  191 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  841 GLU
Chi-restraints excluded: chain A residue  854 VAL
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  891 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain A residue  937 SER
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1003 THR
Chi-restraints excluded: chain A residue 1004 THR
Chi-restraints excluded: chain A residue 1027 PHE
Chi-restraints excluded: chain A residue 1038 THR
Chi-restraints excluded: chain A residue 1199 PHE
Chi-restraints excluded: chain A residue 1220 ILE
Chi-restraints excluded: chain A residue 1290 THR
Chi-restraints excluded: chain A residue 1302 ILE
Chi-restraints excluded: chain A residue 1338 ILE
Chi-restraints excluded: chain A residue 1407 SER
Chi-restraints excluded: chain A residue 1417 ILE
Chi-restraints excluded: chain A residue 1425 ASP
Chi-restraints excluded: chain A residue 1428 MET
Chi-restraints excluded: chain A residue 1462 ILE
Chi-restraints excluded: chain A residue 1524 LYS
Chi-restraints excluded: chain A residue 1736 ILE
Chi-restraints excluded: chain A residue 1751 TYR
Chi-restraints excluded: chain A residue 1771 THR
Chi-restraints excluded: chain A residue 1823 VAL
Chi-restraints excluded: chain A residue 1863 SER
Chi-restraints excluded: chain A residue 1883 CYS
Chi-restraints excluded: chain A residue 1902 GLN
Chi-restraints excluded: chain A residue 1912 LEU
Chi-restraints excluded: chain A residue 1913 VAL
Chi-restraints excluded: chain A residue 1922 ASN
Chi-restraints excluded: chain A residue 2021 LEU
Chi-restraints excluded: chain A residue 2057 GLN
Chi-restraints excluded: chain A residue 2082 TYR
Chi-restraints excluded: chain H residue   50 TRP
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  130 THR
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain L residue   31 SER
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue  170 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 124 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 98 optimal weight:   30.0000
   chunk 116 optimal weight:   20.0000
   chunk 28 optimal weight:    0.0010
   chunk 100 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0670
   overall best weight:    0.7326

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 951 HIS
H  31 ASN
** L  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.158125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.123487 restraints weight = 20183.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.122980 restraints weight = 13537.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.124313 restraints weight = 10846.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.124968 restraints weight = 8771.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.125360 restraints weight = 8107.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  10241  Z= 0.121
  Angle     :  0.665  11.549  13882  Z= 0.326
  Chirality :  0.045   0.302   1556
  Planarity :  0.004   0.057   1774
  Dihedral  :  5.372  57.417   1372
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.14 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.13 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.24), residues: 1246
  helix:  0.75 (0.32), residues: 266
  sheet: -0.03 (0.29), residues: 339
  loop : -0.88 (0.25), residues: 641

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG H  22 
 TYR   0.017   0.001   TYR L 141 
 PHE   0.012   0.001   PHE L 140 
 TRP   0.006   0.001   TRP A1899 
 HIS   0.005   0.001   HIS A 951 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.12 (10237)
  covalent geometry    : angle       0.66506 /  0.33 (13874)
  SS BOND              : bond        0.00260 /  0.13 (    4)
  SS BOND              : angle       0.58967 /  0.42 (    8)
  hydrogen bonds       : bond        0.03174 /  2.16 (  342)
  hydrogen bonds       : angle       5.13438 /  3.64 (  897)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2253.97 seconds
wall clock time: 39 minutes 36.68 seconds (2376.68 seconds total)