Starting phenix.real_space_refine
on Fri Oct 23 05:00:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y7i_72656/10_2026/9y7i_72656.map"
  }
  resolution = 3.73
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      47      5.16       5
     C    5240      2.51       5
     N    1412      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8132
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1101, 8101
          Classifications: {'peptide': 1101}
          Incomplete info: {'truncation_to_alanine': 200}
          Link IDs: {'PTRANS': 47, 'TRANS': 1053}
          Chain breaks: 15
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 726
          Unresolved non-hydrogen angles: 899
          Unresolved non-hydrogen dihedrals: 605
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 12, 'ARG:plan': 13, 'GLN:plan1': 14, 'ASP:plan': 13, 'GLU:plan': 22, 'PHE:plan': 5, 'HIS:plan': 9, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 380
      Conformer: "B"
        Number of residues, atoms: 1101, 8101
          Classifications: {'peptide': 1101}
          Incomplete info: {'truncation_to_alanine': 200}
          Link IDs: {'PTRANS': 47, 'TRANS': 1053}
          Chain breaks: 15
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 726
          Unresolved non-hydrogen angles: 899
          Unresolved non-hydrogen dihedrals: 605
          Unresolved non-hydrogen chiralities: 49
          Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 12, 'ARG:plan': 13, 'GLN:plan1': 14, 'ASP:plan': 13, 'GLU:plan': 22, 'PHE:plan': 5, 'HIS:plan': 9, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 380
          bond proxies already assigned to first conformer: 8203
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'A1N': 1, 'GNP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  AARG A1441 " occ=0.64
      ... (20 atoms not shown)
      pdb=" NH2BARG A1441 " occ=0.36
    residue:
      pdb=" N  ALYS A1539 " occ=0.66
      ... (8 atoms not shown)
      pdb=" CB BLYS A1539 " occ=0.34
    residue:
      pdb=" N  AARG A1550 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BARG A1550 " occ=0.50
    residue:
      pdb=" N  AHIS A1998 " occ=0.16
      ... (18 atoms not shown)
      pdb=" NE2BHIS A1998 " occ=0.84
  Time building chain proxies: 3.06, per 1000 atoms: 0.37
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (77.605, 97.24, 143.055, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P       3     15.00
     O    1490      8.00
     N    1412      7.00
     C    5240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 526.6 milliseconds
  

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 18 sheets defined
      25.5% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1349 through 1355
    Processing helix  chain 'A' and resid 1425 through 1440
      removed outlier: 3.590A  pdb=" N   LYS A1432 " --> pdb=" O   VAL A1428 " (cutoff:3.500A)
      Proline residue:  A1433  - end of helix
      removed outlier: 3.804A  pdb=" N   ALA A1440 " --> pdb=" O   PHE A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1473
      removed outlier: 3.788A  pdb=" N   ILE A1469 " --> pdb=" O   CYS A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1497 through 1508
    Processing helix  chain 'A' and resid 1527 through 1536
    Processing helix  chain 'A' and resid 1550 through 1561
      removed outlier: 3.752A  pdb=" N   GLN A1561 " --> pdb=" O   VAL A1557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1567 through 1572
    Processing helix  chain 'A' and resid 1575 through 1580
      removed outlier: 3.787A  pdb=" N   GLY A1580 " --> pdb=" O   LEU A1576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1599 through 1607
      removed outlier: 4.219A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1651 through 1656
      removed outlier: 3.978A  pdb=" N   PHE A1656 " --> pdb=" O   LEU A1652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1707 through 1715
    Processing helix  chain 'A' and resid 1770 through 1791
      removed outlier: 4.049A  pdb=" N   ILE A1775 " --> pdb=" O   ARG A1771 " (cutoff:3.500A)
      removed outlier: 4.703A  pdb=" N   LEU A1776 " --> pdb=" O   LYS A1772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1796
    Processing helix  chain 'A' and resid 1856 through 1861
      removed outlier: 3.639A  pdb=" N   ILE A1860 " --> pdb=" O   ALA A1856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1880 through 1882
      No H-bonds generated for 'chain 'A' and resid 1880 through 1882'
    Processing helix  chain 'A' and resid 1914 through 1925
      removed outlier: 4.323A  pdb=" N   GLU A1920 " --> pdb=" O   LEU A1916 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   VAL A1923 " --> pdb=" O   GLN A1919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1955 through 1962
    Processing helix  chain 'A' and resid 1967 through 1987
      removed outlier: 4.386A  pdb=" N   ARG A1973 " --> pdb=" O   THR A1969 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A1974 " --> pdb=" O   LEU A1970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2051 through 2053
      No H-bonds generated for 'chain 'A' and resid 2051 through 2053'
    Processing helix  chain 'A' and resid 2054 through 2068
      removed outlier: 3.910A  pdb=" N   SER A2058 " --> pdb=" O   ALA A2054 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR A2068 " --> pdb=" O   TYR A2064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2072 through 2077
    Processing helix  chain 'A' and resid 2094 through 2100
      removed outlier: 3.562A  pdb=" N   GLU A2098 " --> pdb=" O   ASP A2094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2107 through 2112
    Processing helix  chain 'A' and resid 2124 through 2131
      removed outlier: 3.547A  pdb=" N   PHE A2129 " --> pdb=" O   SER A2125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2134 through 2139
      removed outlier: 3.592A  pdb=" N   VAL A2138 " --> pdb=" O   SER A2134 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   CYS A2139 " --> pdb=" O   ALA A2135 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2134 through 2139'
    Processing helix  chain 'A' and resid 2278 through 2282
      removed outlier: 4.178A  pdb=" N   LYS A2281 " --> pdb=" O   LYS A2278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2339 through 2344
      removed outlier: 3.883A  pdb=" N   GLN A2342 " --> pdb=" O   ARG A2339 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   LEU A2343 " --> pdb=" O   THR A2340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
      removed outlier: 3.634A  pdb=" N   SER A2350 " --> pdb=" O   TYR A2346 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ASP A2351 " --> pdb=" O   ALA A2347 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2346 through 2351'
    Processing helix  chain 'A' and resid 2389 through 2395
      removed outlier: 3.831A  pdb=" N   GLU A2395 " --> pdb=" O   HIS A2391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2499 through 2525
      removed outlier: 3.912A  pdb=" N   GLN A2505 " --> pdb=" O   PRO A2501 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASN A2506 " --> pdb=" O   HIS A2502 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A2512 " --> pdb=" O   GLU A2508 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ARG A2514 " --> pdb=" O   HIS A2510 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLU A2516 " --> pdb=" O   GLU A2512 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLU A2519 " --> pdb=" O   LYS A2515 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   MET A2521 " --> pdb=" O   LEU A2517 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ARG A2522 " --> pdb=" O   ALA A2518 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG A2523 " --> pdb=" O   GLU A2519 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   THR A2524 " --> pdb=" O   LYS A2520 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER A2525 " --> pdb=" O   MET A2521 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1372 through 1378
      removed outlier: 3.669A  pdb=" N   TRP A1376 " --> pdb=" O   LEU A1390 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A1390 " --> pdb=" O   TRP A1376 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN A1391 " --> pdb=" O   MET A1335 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A1414 " --> pdb=" O   LYS A1336 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A1416 " --> pdb=" O   MET A1338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1547 through 1549
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1691 through 1693
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1696 through 1697
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1733 through 1734
      removed outlier: 3.716A  pdb=" N   GLY A1737 " --> pdb=" O   TRP A1734 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1811 through 1812
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1839 through 1842
      removed outlier: 3.907A  pdb=" N   ASN A1842 " --> pdb=" O   GLN A1845 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1875 through 1877
      removed outlier: 3.695A  pdb=" N   GLY A1886 " --> pdb=" O   VAL A1893 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ARG A1895 " --> pdb=" O   LEU A1884 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   LEU A1884 " --> pdb=" O   ARG A1895 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1875 through 1877
      removed outlier: 3.660A  pdb=" N   LEU A1945 " --> pdb=" O   LYS A1906 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   GLU A1948 " --> pdb=" O   LEU A1935 " (cutoff:3.500A)
      removed outlier: 8.114A  pdb=" N   LEU A1935 " --> pdb=" O   GLU A1948 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1953 through 1954
      removed outlier: 3.549A  pdb=" N   GLY A1953 " --> pdb=" O   LEU A2002 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2140 through 2145
      removed outlier: 6.730A  pdb=" N   VAL A2495 " --> pdb=" O   THR A2141 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ARG A2143 " --> pdb=" O   LEU A2493 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU A2493 " --> pdb=" O   ARG A2143 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   LEU A2145 " --> pdb=" O   SER A2491 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   SER A2491 " --> pdb=" O   LEU A2145 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   VAL A2469 " --> pdb=" O   THR A2460 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   THR A2460 " --> pdb=" O   VAL A2469 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU A2471 " --> pdb=" O   MET A2458 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A2458 " --> pdb=" O   LEU A2471 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU A2473 " --> pdb=" O   ARG A2456 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2155 through 2157
      removed outlier: 3.562A  pdb=" N   LEU A2182 " --> pdb=" O   ILE A2167 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2199 through 2202
      removed outlier: 4.188A  pdb=" N   CYS A2201 " --> pdb=" O   GLY A2218 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY A2218 " --> pdb=" O   CYS A2201 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 2199 through 2202
      removed outlier: 4.188A  pdb=" N   CYS A2201 " --> pdb=" O   GLY A2218 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY A2218 " --> pdb=" O   CYS A2201 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS A2236 " --> pdb=" O   VAL A2226 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 2245 through 2249
      removed outlier: 4.615A  pdb=" N   LYS A2271 " --> pdb=" O   THR A2267 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS A2289 " --> pdb=" O   ILE A2274 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 2300 through 2305
      removed outlier: 4.521A  pdb=" N   CYS A2302 " --> pdb=" O   GLY A2318 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY A2318 " --> pdb=" O   CYS A2302 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER A2325 " --> pdb=" O   LYS A2334 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   LYS A2334 " --> pdb=" O   SER A2325 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2354 through 2358
      removed outlier: 3.917A  pdb=" N   THR A2356 " --> pdb=" O   ALA A2366 " (cutoff:3.500A)
      removed outlier: 5.011A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY A2385 " --> pdb=" O   VAL A2375 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 2417 through 2420
      removed outlier: 3.660A  pdb=" N   ALA A2424 " --> pdb=" O   GLN A2420 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG A2446 " --> pdb=" O   LEU A2436 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ASP A2438 " --> pdb=" O   LEU A2444 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU A2444 " --> pdb=" O   ASP A2438 " (cutoff:3.500A)

    252 hydrogen bonds defined for protein.
    684 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: 1.62

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2659
        1.34 -     1.46: 1695
        1.46 -     1.58: 3911
        1.58 -     1.70: 3
        1.70 -     1.82: 73
  Bond restraints: 8341
  Sorted by residual:
  bond pdb=" N3B GNP A2601 "
       pdb=" PG  GNP A2601 "
    ideal  model  delta    sigma   weight residual
    1.801  1.709  0.092 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" O5' GNP A2601 "
       pdb=" PA  GNP A2601 "
    ideal  model  delta    sigma   weight residual
    1.660  1.577  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" N3B GNP A2601 "
       pdb=" PB  GNP A2601 "
    ideal  model  delta    sigma   weight residual
    1.681  1.636  0.045 2.00e-02 2.50e+03 5.11e+00
  bond pdb=" O3A GNP A2601 "
       pdb=" PB  GNP A2601 "
    ideal  model  delta    sigma   weight residual
    1.687  1.645  0.042 2.00e-02 2.50e+03 4.32e+00
  bond pdb=" C   ASP A1863 "
       pdb=" N   LEU A1864 "
    ideal  model  delta    sigma   weight residual
    1.331  1.274  0.057 2.83e-02 1.25e+03 4.04e+00
  ... (remaining 8336 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.13: 11122
        3.13 -     6.26: 195
        6.26 -     9.39: 36
        9.39 -    12.52: 6
       12.52 -    15.64: 2
  Bond angle restraints: 11361
  Sorted by residual:
  angle pdb=" N   VAL A2107 "
        pdb=" CA  VAL A2107 "
        pdb=" C   VAL A2107 "
      ideal   model   delta    sigma   weight residual
     113.53  105.67    7.86 9.80e-01 1.04e+00 6.43e+01
  angle pdb=" N   MET A1989 "
        pdb=" CA  MET A1989 "
        pdb=" CB  MET A1989 "
      ideal   model   delta    sigma   weight residual
     114.17  107.31    6.86 1.14e+00 7.69e-01 3.62e+01
  angle pdb=" C   ASP A1828 "
        pdb=" N   ASP A1829 "
        pdb=" CA  ASP A1829 "
      ideal   model   delta    sigma   weight residual
     121.54  130.63   -9.09 1.91e+00 2.74e-01 2.27e+01
  angle pdb=" CA  LEU A1749 "
        pdb=" CB  LEU A1749 "
        pdb=" CG  LEU A1749 "
      ideal   model   delta    sigma   weight residual
     116.30  131.94  -15.64 3.50e+00 8.16e-02 2.00e+01
  angle pdb=" N   LEU A2132 "
        pdb=" CA  LEU A2132 "
        pdb=" C   LEU A2132 "
      ideal   model   delta    sigma   weight residual
     114.31  108.55    5.76 1.29e+00 6.01e-01 1.99e+01
  ... (remaining 11356 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.73: 4813
       28.73 -    57.45: 165
       57.45 -    86.18: 17
       86.18 -   114.90: 3
      114.90 -   143.63: 1
  Dihedral angle restraints: 4999
    sinusoidal: 1781
      harmonic: 3218
  Sorted by residual:
  dihedral pdb=" CA  ARG A1941 "
           pdb=" C   ARG A1941 "
           pdb=" N   PRO A1942 "
           pdb=" CA  PRO A1942 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.04   30.96     0      5.00e+00 4.00e-02 3.83e+01
  dihedral pdb=" CA  MET A2106 "
           pdb=" C   MET A2106 "
           pdb=" N   VAL A2107 "
           pdb=" CA  VAL A2107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.28   24.72     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  ALA A1988 "
           pdb=" C   ALA A1988 "
           pdb=" N   MET A1989 "
           pdb=" CA  MET A1989 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.55   24.45     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 4996 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1263
       0.104 -    0.207: 90
       0.207 -    0.310: 2
       0.310 -    0.414: 0
       0.414 -    0.517: 2
  Chirality restraints: 1357
  Sorted by residual:
  chirality pdb=" CB  ILE A1339 "
            pdb=" CA  ILE A1339 "
            pdb=" CG1 ILE A1339 "
            pdb=" CG2 ILE A1339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.13    0.52 2.00e-01 2.50e+01 6.69e+00
  chirality pdb=" CB  ILE A1852 "
            pdb=" CA  ILE A1852 "
            pdb=" CG1 ILE A1852 "
            pdb=" CG2 ILE A1852 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.16    0.49 2.00e-01 2.50e+01 5.95e+00
  chirality pdb=" CB  ILE A2049 "
            pdb=" CA  ILE A2049 "
            pdb=" CG1 ILE A2049 "
            pdb=" CG2 ILE A2049 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 1354 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A2118 "    0.071 5.00e-02 4.00e+02   1.07e-01 1.82e+01
        pdb=" N   PRO A2119 "   -0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO A2119 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A2119 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A1402 "   -0.007 2.00e-02 2.50e+03   2.54e-02 1.29e+01
        pdb=" CG  TYR A1402 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR A1402 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR A1402 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR A1402 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR A1402 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A1402 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A1402 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A1432 "    0.051 5.00e-02 4.00e+02   7.64e-02 9.35e+00
        pdb=" N   PRO A1433 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A1433 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A1433 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1644
        2.78 -     3.31: 7574
        3.31 -     3.84: 13001
        3.84 -     4.37: 14442
        4.37 -     4.90: 24810
  Nonbonded interactions: 61471
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A2267 "
            pdb=" OD1 ASP A2269 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER A2213 "
            pdb=" OG1 THR A2229 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG  SER A1934 "
            pdb=" OE2 GLU A1948 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASP A2065 "
            pdb=" NH1 ARG A2072 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OG  SER A1951 "
            pdb=" O   PHE A2003 "
     model   vdw
     2.290 3.040
  ... (remaining 61466 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.16 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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
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      :  0.005   0.092   8341  Z= 0.231
  Angle     :  1.063  15.644  11361  Z= 0.536
  Chirality :  0.059   0.517   1357
  Planarity :  0.007   0.107   1431
  Dihedral  : 14.812 143.629   2907
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.38 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.77 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.24), residues: 1081
  helix: -2.48 (0.28), residues: 264
  sheet: -0.79 (0.37), residues: 213
  loop : -2.45 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A2072 
 TYR   0.059   0.003   TYR A1402 
 PHE   0.037   0.002   PHE A2003 
 TRP   0.032   0.003   TRP A1791 
 HIS   0.007   0.001   HIS A1928 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00504 /  0.23 ( 8341)
  covalent geometry    : angle       1.06306 /  0.54 (11361)
  hydrogen bonds       : bond        0.19594 / 13.07 (  250)
  hydrogen bonds       : angle       8.57918 /  5.85 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A 1343 THR cc_start: 0.7490 (p) cc_final: 0.7263 (p)
REVERT: A 1947 MET cc_start: 0.6752 (ptt) cc_final: 0.6339 (ptt)
REVERT: A 1995 LEU cc_start: 0.7721 (tp) cc_final: 0.7205 (tp)
REVERT: A 2241 MET cc_start: 0.5328 (tmm) cc_final: 0.4925 (tmm)
REVERT: A 2326 PHE cc_start: 0.7752 (m-10) cc_final: 0.7513 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0710
  time to fit residues: 14.0080
Evaluate side-chains
  110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106]
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   overall best weight:    0.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1919 GLN
A2113 GLN
A2159 HIS
A2173 HIS
A2391 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.149804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.110450 restraints weight = 65452.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.116480 restraints weight = 23350.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120591 restraints weight = 12823.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.123314 restraints weight = 8682.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.125159 restraints weight = 6706.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3945 r_free = 0.3945    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8341  Z= 0.127
  Angle     :  0.702  14.280  11361  Z= 0.351
  Chirality :  0.046   0.227   1357
  Planarity :  0.005   0.074   1431
  Dihedral  :  7.997 142.729   1217
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  9.07 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.21 %
    Favored  : 89.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.25), residues: 1081
  helix: -1.38 (0.32), residues: 272
  sheet: -0.49 (0.37), residues: 206
  loop : -2.26 (0.24), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1731 
 TYR   0.020   0.001   TYR A1992 
 PHE   0.013   0.001   PHE A1656 
 TRP   0.020   0.002   TRP A1791 
 HIS   0.010   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 8341)
  covalent geometry    : angle       0.70187 /  0.35 (11361)
  hydrogen bonds       : bond        0.03356 /  2.24 (  250)
  hydrogen bonds       : angle       6.04585 /  4.11 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A 1343 THR cc_start: 0.7348 (p) cc_final: 0.7105 (p)
REVERT: A 1866 ARG cc_start: 0.7648 (mmp80) cc_final: 0.7268 (mmp80)
REVERT: A 1947 MET cc_start: 0.7357 (ptt) cc_final: 0.6819 (ptt)
REVERT: A 1995 LEU cc_start: 0.7645 (tp) cc_final: 0.7137 (tp)
REVERT: A 2049 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7798 (tt)
REVERT: A 2241 MET cc_start: 0.5843 (tmm) cc_final: 0.5375 (tmm)
  outliers start: 7
  outliers final: 3
  residues processed: 122
  average time/residue: 0.0751
  time to fit residues: 13.4252
Evaluate side-chains
  112 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1925 CYS
Chi-restraints excluded: chain A residue 2049 ILE
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2358 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [71, 0, 69, 92, 16, 75, 104, 79, 36, 84, 22]
   chunk 71 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    6.9990
   chunk 92 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 75 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1919 GLN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1998 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2047 ASN
A2089 GLN
A2113 GLN
A2173 HIS
A2391 HIS
A2462 GLN
** A2499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.135717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.097693 restraints weight = 47412.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.102508 restraints weight = 19277.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.105844 restraints weight = 11236.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.108138 restraints weight = 7941.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.109558 restraints weight = 6310.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.086   8341  Z= 0.468
  Angle     :  1.108  16.258  11361  Z= 0.559
  Chirality :  0.057   0.215   1357
  Planarity :  0.007   0.082   1431
  Dihedral  :  9.425 144.674   1217
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 22.14
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 12.35 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 12.15 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.23), residues: 1081
  helix: -1.66 (0.31), residues: 271
  sheet: -1.21 (0.34), residues: 217
  loop : -2.66 (0.23), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1731 
 TYR   0.031   0.004   TYR A1733 
 PHE   0.044   0.004   PHE A2003 
 TRP   0.036   0.004   TRP A1791 
 HIS   0.024   0.004   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01050 /  0.47 ( 8341)
  covalent geometry    : angle       1.10781 /  0.56 (11361)
  hydrogen bonds       : bond        0.04704 /  3.19 (  250)
  hydrogen bonds       : angle       6.79690 /  4.59 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A 1732 MET cc_start: 0.8162 (tpp) cc_final: 0.7760 (tpp)
REVERT: A 1919 GLN cc_start: 0.7952 (mt0) cc_final: 0.7749 (mt0)
REVERT: A 1947 MET cc_start: 0.7838 (ptt) cc_final: 0.7527 (ptt)
REVERT: A 2047 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6792 (t0)
REVERT: A 2089 GLN cc_start: 0.5089 (OUTLIER) cc_final: 0.3938 (pm20)
REVERT: A 2241 MET cc_start: 0.6563 (tmm) cc_final: 0.6094 (tmm)
REVERT: A 2397 MET cc_start: 0.5454 (mpp) cc_final: 0.5036 (mmm)
  outliers start: 27
  outliers final: 19
  residues processed: 133
  average time/residue: 0.0561
  time to fit residues: 11.8723
Evaluate side-chains
  121 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1414 LEU
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1582 LEU
Chi-restraints excluded: chain A residue 1749 LEU
Chi-restraints excluded: chain A residue 1925 CYS
Chi-restraints excluded: chain A residue 2047 ASN
Chi-restraints excluded: chain A residue 2089 GLN
Chi-restraints excluded: chain A residue 2144 ILE
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2380 THR
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2463 LEU
Chi-restraints excluded: chain A residue 2471 LEU
Chi-restraints excluded: chain A residue 2489 ILE
Chi-restraints excluded: chain A residue 2493 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [18, 87, 35, 90, 95, 93, 108, 94, 63, 92, 107]
   chunk 18 optimal weight:    9.9990
   chunk 87 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0770
   chunk 90 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   chunk 108 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    0.7138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1872 ASN
A2047 ASN
A2089 GLN
A2113 GLN
A2159 HIS
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.142494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.103918 restraints weight = 58983.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.109630 restraints weight = 21140.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.113534 restraints weight = 11662.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.116200 restraints weight = 7923.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.118077 restraints weight = 6124.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8341  Z= 0.136
  Angle     :  0.745  14.879  11361  Z= 0.369
  Chirality :  0.047   0.159   1357
  Planarity :  0.005   0.062   1431
  Dihedral  :  8.378 142.819   1217
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.45 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.88 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.25), residues: 1081
  helix: -0.76 (0.35), residues: 263
  sheet: -1.18 (0.35), residues: 219
  loop : -2.43 (0.23), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1731 
 TYR   0.024   0.002   TYR A1992 
 PHE   0.017   0.002   PHE A2003 
 TRP   0.031   0.002   TRP A1602 
 HIS   0.023   0.002   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 8341)
  covalent geometry    : angle       0.74479 /  0.37 (11361)
  hydrogen bonds       : bond        0.02934 /  1.95 (  250)
  hydrogen bonds       : angle       5.70578 /  3.85 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A 1732 MET cc_start: 0.7750 (tpp) cc_final: 0.7505 (tpp)
REVERT: A 2047 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6527 (t0)
REVERT: A 2065 ASP cc_start: 0.8347 (t0) cc_final: 0.8121 (t0)
REVERT: A 2179 LEU cc_start: 0.8856 (tt) cc_final: 0.8555 (mm)
REVERT: A 2241 MET cc_start: 0.6444 (tmm) cc_final: 0.5994 (tmm)
REVERT: A 2397 MET cc_start: 0.5273 (mpp) cc_final: 0.4913 (mmm)
REVERT: A 2459 MET cc_start: 0.8001 (ppp) cc_final: 0.7258 (ppp)
  outliers start: 15
  outliers final: 7
  residues processed: 124
  average time/residue: 0.0622
  time to fit residues: 11.7154
Evaluate side-chains
  114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1648 GLN
Chi-restraints excluded: chain A residue 2047 ASN
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [67, 88, 4, 3, 12, 94, 109, 101, 53, 18, 27]
   chunk 67 optimal weight:    2.9990
   chunk 88 optimal weight:    0.5980
   chunk 4 optimal weight:   20.0000
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 109 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1872 ASN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1998 HIS    B
A1999 ASN
A2047 ASN
A2089 GLN
A2113 GLN
A2159 HIS
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.140695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.103026 restraints weight = 48069.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.108214 restraints weight = 19146.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.111748 restraints weight = 11026.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.114150 restraints weight = 7688.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.115843 restraints weight = 6026.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8341  Z= 0.200
  Angle     :  0.774  14.720  11361  Z= 0.384
  Chirality :  0.047   0.167   1357
  Planarity :  0.005   0.048   1431
  Dihedral  :  8.306 142.499   1217
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.32 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.75 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.25), residues: 1081
  helix: -0.79 (0.34), residues: 266
  sheet: -1.15 (0.35), residues: 220
  loop : -2.45 (0.23), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1943 
 TYR   0.012   0.002   TYR A1402 
 PHE   0.022   0.002   PHE A2003 
 TRP   0.016   0.002   TRP A1602 
 HIS   0.016   0.002   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.20 ( 8341)
  covalent geometry    : angle       0.77412 /  0.38 (11361)
  hydrogen bonds       : bond        0.03026 /  2.02 (  250)
  hydrogen bonds       : angle       5.77267 /  3.88 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A 1732 MET cc_start: 0.7978 (tpp) cc_final: 0.7720 (tpp)
REVERT: A 2017 ASP cc_start: 0.7968 (t70) cc_final: 0.7377 (t70)
REVERT: A 2179 LEU cc_start: 0.8850 (tt) cc_final: 0.8573 (mm)
REVERT: A 2241 MET cc_start: 0.6559 (tmm) cc_final: 0.6086 (tmm)
REVERT: A 2397 MET cc_start: 0.5377 (mpp) cc_final: 0.4981 (mmm)
REVERT: A 2459 MET cc_start: 0.7947 (ppp) cc_final: 0.7147 (ppp)
  outliers start: 22
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0674
  time to fit residues: 12.7641
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1390 LEU
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1648 GLN
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1830 LEU
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2390 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2489 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [102, 63, 89, 33, 82, 100, 11, 23, 35, 69, 92]
   chunk 102 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 89 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 82 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 69 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1872 ASN
A1919 GLN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1999 ASN
A2047 ASN
A2159 HIS
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.143829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.106747 restraints weight = 49538.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.112172 restraints weight = 18725.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.115830 restraints weight = 10510.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.118349 restraints weight = 7231.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.120052 restraints weight = 5620.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3832
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3832 r_free = 0.3832    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3832 r_free = 0.3832    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3832
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8341  Z= 0.132
  Angle     :  0.714  14.007  11361  Z= 0.352
  Chirality :  0.046   0.177   1357
  Planarity :  0.005   0.056   1431
  Dihedral  :  8.108 142.620   1217
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.64 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.14 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.25), residues: 1081
  helix: -0.63 (0.35), residues: 266
  sheet: -1.07 (0.35), residues: 221
  loop : -2.33 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A2039 
 TYR   0.026   0.001   TYR A1718 
 PHE   0.016   0.001   PHE A2003 
 TRP   0.015   0.002   TRP A1791 
 HIS   0.021   0.002   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.13 ( 8341)
  covalent geometry    : angle       0.71382 /  0.35 (11361)
  hydrogen bonds       : bond        0.02691 /  1.78 (  250)
  hydrogen bonds       : angle       5.55798 /  3.74 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A 1732 MET cc_start: 0.7865 (tpp) cc_final: 0.7560 (tpp)
REVERT: A 2017 ASP cc_start: 0.8016 (t70) cc_final: 0.7362 (t70)
REVERT: A 2151 ILE cc_start: 0.8004 (mp) cc_final: 0.7667 (pt)
REVERT: A 2179 LEU cc_start: 0.8859 (tt) cc_final: 0.8576 (mm)
REVERT: A 2241 MET cc_start: 0.6526 (tmm) cc_final: 0.6061 (tmm)
REVERT: A 2397 MET cc_start: 0.5406 (mpp) cc_final: 0.5030 (mmm)
REVERT: A 2459 MET cc_start: 0.7938 (ppp) cc_final: 0.7219 (ppp)
  outliers start: 17
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0655
  time to fit residues: 12.6556
Evaluate side-chains
  123 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1648 GLN
Chi-restraints excluded: chain A residue 1705 TRP
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1830 LEU
Chi-restraints excluded: chain A residue 1872 ASN
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 2145 LEU
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2455 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [93, 22, 88, 34, 56, 55, 15, 90, 19, 13, 63]
   chunk 93 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 88 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 90 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0970
   chunk 13 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1872 ASN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2159 HIS
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.139834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.100054 restraints weight = 71004.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.105584 restraints weight = 24078.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.109354 restraints weight = 13179.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.111906 restraints weight = 9007.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.113764 restraints weight = 6982.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3760 r_free = 0.3760    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8341  Z= 0.139
  Angle     :  0.717  16.050  11361  Z= 0.352
  Chirality :  0.046   0.190   1357
  Planarity :  0.004   0.048   1431
  Dihedral  :  8.039 142.672   1217
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.10 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.26 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.25), residues: 1081
  helix: -0.64 (0.34), residues: 271
  sheet: -1.04 (0.35), residues: 218
  loop : -2.28 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A2039 
 TYR   0.013   0.001   TYR A1992 
 PHE   0.016   0.002   PHE A2003 
 TRP   0.015   0.002   TRP A1791 
 HIS   0.012   0.001   HIS A2391 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 8341)
  covalent geometry    : angle       0.71707 /  0.35 (11361)
  hydrogen bonds       : bond        0.02677 /  1.76 (  250)
  hydrogen bonds       : angle       5.46856 /  3.67 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1436 PHE cc_start: 0.7786 (m-80) cc_final: 0.7506 (m-80)
REVERT: A 1707 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7468 (mtt180)
REVERT: A 1732 MET cc_start: 0.7843 (tpp) cc_final: 0.7527 (tpp)
REVERT: A 2017 ASP cc_start: 0.7981 (t70) cc_final: 0.7332 (t70)
REVERT: A 2151 ILE cc_start: 0.8002 (mp) cc_final: 0.7676 (pt)
REVERT: A 2179 LEU cc_start: 0.8931 (tt) cc_final: 0.8653 (mm)
REVERT: A 2241 MET cc_start: 0.6492 (tmm) cc_final: 0.5972 (tmm)
REVERT: A 2397 MET cc_start: 0.5455 (mpp) cc_final: 0.5061 (mmm)
REVERT: A 2459 MET cc_start: 0.7942 (ppp) cc_final: 0.7235 (ppp)
  outliers start: 22
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0656
  time to fit residues: 12.5558
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1648 GLN
Chi-restraints excluded: chain A residue 1705 TRP
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1830 LEU
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1925 CYS
Chi-restraints excluded: chain A residue 2145 LEU
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2301 MET
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2495 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [98, 79, 100, 32, 109, 37, 17, 52, 60, 77, 84]
   chunk 98 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 109 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0010
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   overall best weight:    0.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1657 GLN
A1872 ASN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.141390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.102074 restraints weight = 63337.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.107509 restraints weight = 23502.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.111248 restraints weight = 13192.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.113803 restraints weight = 9068.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.115431 restraints weight = 7089.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3790 r_free = 0.3790    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3790 r_free = 0.3790    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7139
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8341  Z= 0.116
  Angle     :  0.702  15.609  11361  Z= 0.342
  Chirality :  0.046   0.200   1357
  Planarity :  0.004   0.048   1431
  Dihedral  :  7.940 142.654   1217
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.10 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.77 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.24 (0.26), residues: 1081
  helix: -0.58 (0.34), residues: 272
  sheet: -0.93 (0.35), residues: 223
  loop : -2.21 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2039 
 TYR   0.017   0.001   TYR A1992 
 PHE   0.014   0.001   PHE A2326 
 TRP   0.016   0.002   TRP A1791 
 HIS   0.013   0.001   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 8341)
  covalent geometry    : angle       0.70181 /  0.34 (11361)
  hydrogen bonds       : bond        0.02551 /  1.68 (  250)
  hydrogen bonds       : angle       5.33735 /  3.59 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1436 PHE cc_start: 0.7797 (m-80) cc_final: 0.7459 (m-80)
REVERT: A 1707 ARG cc_start: 0.7838 (mtp85) cc_final: 0.7543 (mtt180)
REVERT: A 1732 MET cc_start: 0.7685 (tpp) cc_final: 0.7355 (tpp)
REVERT: A 2017 ASP cc_start: 0.7927 (t70) cc_final: 0.7033 (t70)
REVERT: A 2151 ILE cc_start: 0.7941 (mp) cc_final: 0.7648 (pt)
REVERT: A 2179 LEU cc_start: 0.8940 (tt) cc_final: 0.8667 (mm)
REVERT: A 2241 MET cc_start: 0.6425 (tmm) cc_final: 0.5871 (tmm)
REVERT: A 2397 MET cc_start: 0.5478 (mpp) cc_final: 0.5124 (mmm)
REVERT: A 2459 MET cc_start: 0.7879 (ppp) cc_final: 0.7204 (ppp)
  outliers start: 18
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0687
  time to fit residues: 13.1416
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1339 ILE
Chi-restraints excluded: chain A residue 1365 GLN
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1418 VAL
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1705 TRP
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1830 LEU
Chi-restraints excluded: chain A residue 2145 LEU
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2455 VAL
Chi-restraints excluded: chain A residue 2495 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [50, 66, 99, 74, 65, 34, 92, 106, 109, 96, 10]
   chunk 50 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 99 optimal weight:    0.4980
   chunk 74 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0770
   chunk 106 optimal weight:    1.9990
   chunk 109 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0470
   overall best weight:    0.3036

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2159 HIS
A2173 HIS
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.144094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.104923 restraints weight = 72474.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.110828 restraints weight = 24448.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.114860 restraints weight = 13121.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.117631 restraints weight = 8810.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.119502 restraints weight = 6746.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8341  Z= 0.107
  Angle     :  0.692  15.945  11361  Z= 0.335
  Chirality :  0.045   0.200   1357
  Planarity :  0.004   0.048   1431
  Dihedral  :  7.713 142.427   1217
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.64 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 18.41 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.14 (0.26), residues: 1081
  helix: -0.58 (0.34), residues: 275
  sheet: -0.78 (0.36), residues: 212
  loop : -2.13 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2039 
 TYR   0.019   0.001   TYR A1992 
 PHE   0.014   0.001   PHE A2326 
 TRP   0.018   0.002   TRP A1602 
 HIS   0.014   0.001   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 8341)
  covalent geometry    : angle       0.69222 /  0.34 (11361)
  hydrogen bonds       : bond        0.02480 /  1.63 (  250)
  hydrogen bonds       : angle       5.17960 /  3.48 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1707 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7311 (mtt180)
REVERT: A 1732 MET cc_start: 0.7596 (tpp) cc_final: 0.7297 (tpp)
REVERT: A 2179 LEU cc_start: 0.8914 (tt) cc_final: 0.8630 (mm)
REVERT: A 2241 MET cc_start: 0.6225 (tmm) cc_final: 0.5713 (tmm)
REVERT: A 2397 MET cc_start: 0.5397 (mpp) cc_final: 0.5140 (mmm)
REVERT: A 2459 MET cc_start: 0.7777 (ppp) cc_final: 0.7229 (ppp)
  outliers start: 18
  outliers final: 16
  residues processed: 129
  average time/residue: 0.0659
  time to fit residues: 12.7633
Evaluate side-chains
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1365 GLN
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1648 GLN
Chi-restraints excluded: chain A residue 1705 TRP
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1830 LEU
Chi-restraints excluded: chain A residue 1893 VAL
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1925 CYS
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 2145 LEU
Chi-restraints excluded: chain A residue 2173 HIS
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2495 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [85, 82, 97, 100, 35, 77, 83, 12, 28, 89, 26]
   chunk 85 optimal weight:    9.9990
   chunk 82 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0060
   chunk 35 optimal weight:    0.0870
   chunk 77 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 28 optimal weight:   30.0000
   chunk 89 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.3978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1648 GLN
** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2173 HIS
A2391 HIS
** A2502 HIS ** 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 = 0.4199 r_free = 0.4199 target = 0.143903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.105905 restraints weight = 52884.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.111262 restraints weight = 21341.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.114825 restraints weight = 12335.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.117357 restraints weight = 8636.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.119029 restraints weight = 6816.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097   8341  Z= 0.237
  Angle     :  1.104  59.196  11361  Z= 0.643
  Chirality :  0.077   2.118   1357
  Planarity :  0.007   0.221   1431
  Dihedral  :  7.730 142.646   1217
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.73 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.54 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.26), residues: 1081
  helix: -0.59 (0.34), residues: 275
  sheet: -0.78 (0.36), residues: 212
  loop : -2.15 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2039 
 TYR   0.018   0.001   TYR A1992 
 PHE   0.013   0.001   PHE A2326 
 TRP   0.017   0.002   TRP A1602 
 HIS   0.372   0.012   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.24 ( 8341)
  covalent geometry    : angle       1.10441 /  0.64 (11361)
  hydrogen bonds       : bond        0.02513 /  1.65 (  250)
  hydrogen bonds       : angle       5.18154 /  3.48 (  684)

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

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

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2162 Ramachandran restraints generated.
    1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1707 ARG cc_start: 0.7768 (mtp85) cc_final: 0.7336 (mtt180)
REVERT: A 1732 MET cc_start: 0.7621 (tpp) cc_final: 0.7324 (tpp)
REVERT: A 2017 ASP cc_start: 0.7610 (t0) cc_final: 0.6552 (t70)
REVERT: A 2179 LEU cc_start: 0.8918 (tt) cc_final: 0.8634 (mm)
REVERT: A 2241 MET cc_start: 0.6234 (tmm) cc_final: 0.5709 (tmm)
REVERT: A 2397 MET cc_start: 0.5416 (mpp) cc_final: 0.5160 (mmm)
REVERT: A 2459 MET cc_start: 0.7785 (ppp) cc_final: 0.7251 (ppp)
  outliers start: 17
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0628
  time to fit residues: 12.2538
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1365 GLN
Chi-restraints excluded: chain A residue 1547 VAL
Chi-restraints excluded: chain A residue 1705 TRP
Chi-restraints excluded: chain A residue 1750 VAL
Chi-restraints excluded: chain A residue 1893 VAL
Chi-restraints excluded: chain A residue 1924 LEU
Chi-restraints excluded: chain A residue 1925 CYS
Chi-restraints excluded: chain A residue 1947 MET
Chi-restraints excluded: chain A residue 2145 LEU
Chi-restraints excluded: chain A residue 2202 LEU
Chi-restraints excluded: chain A residue 2358 VAL
Chi-restraints excluded: chain A residue 2495 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks: [24, 0, 84, 31, 97, 47, 108, 43, 8, 36, 70]
   chunk 24 optimal weight:    0.1980
   chunk 0 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 31 optimal weight:    0.2980
   chunk 97 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0070
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.3598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2391 HIS
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.143706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.105478 restraints weight = 58752.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.110949 restraints weight = 22743.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.114625 restraints weight = 12938.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.117161 restraints weight = 8981.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.118774 restraints weight = 7034.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3839 r_free = 0.3839    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.097   8341  Z= 0.237
  Angle     :  1.104  59.196  11361  Z= 0.643
  Chirality :  0.077   2.118   1357
  Planarity :  0.007   0.221   1431
  Dihedral  :  7.730 142.646   1217
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 11.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.73 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.05 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.26), residues: 1081
  helix: -0.59 (0.34), residues: 275
  sheet: -0.78 (0.36), residues: 212
  loop : -2.15 (0.25), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A2039 
 TYR   0.018   0.001   TYR A1992 
 PHE   0.013   0.001   PHE A2326 
 TRP   0.017   0.002   TRP A1602 
 HIS   0.372   0.012   HIS A2173 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.24 ( 8341)
  covalent geometry    : angle       1.10441 /  0.64 (11361)
  hydrogen bonds       : bond        0.02513 /  1.65 (  250)
  hydrogen bonds       : angle       5.18154 /  3.48 (  684)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1841.20 seconds
wall clock time: 32 minutes 6.14 seconds (1926.14 seconds total)