Starting phenix.real_space_refine
on Fri Oct 23 07:49:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ycd_72768/10_2026/9ycd_72768.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5513      2.51       5
     N    1490      2.21       5
     O    1547      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 8602
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8574
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1117, 8548
          Classifications: {'peptide': 1117}
          Incomplete info: {'truncation_to_alanine': 99}
          Link IDs: {'PTRANS': 50, 'TRANS': 1066}
          Chain breaks: 14
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 382
          Unresolved non-hydrogen angles: 478
          Unresolved non-hydrogen dihedrals: 319
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 8, 'ARG:plan': 4, 'ASN:plan1': 6, 'GLU:plan': 19, 'PHE:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 233
      Conformer: "B"
        Number of residues, atoms: 1117, 8548
          Classifications: {'peptide': 1117}
          Incomplete info: {'truncation_to_alanine': 99}
          Link IDs: {'PTRANS': 50, 'TRANS': 1066}
          Chain breaks: 14
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 382
          Unresolved non-hydrogen angles: 478
          Unresolved non-hydrogen dihedrals: 319
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'ASP:plan': 9, 'GLN:plan1': 8, 'ARG:plan': 4, 'ASN:plan1': 6, 'GLU:plan': 19, 'PHE:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 233
          bond proxies already assigned to first conformer: 8672
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'A1N': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A1915 " occ=0.67
      ... (20 atoms not shown)
      pdb=" NH2BARG A1915 " occ=0.33
    residue:
      pdb=" N  AHIS A1998 " occ=0.67
      ... (18 atoms not shown)
      pdb=" NE2BHIS A1998 " occ=0.33
  Time building chain proxies: 2.50, per 1000 atoms: 0.29
  Number of scatterers: 8602
  At special positions: 0
  Unit cell: (74.1, 94.05, 143.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1547      8.00
     N    1490      7.00
     C    5513      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: 0.51
  Conformation dependent library (CDL) restraints added in 453.8 milliseconds
  

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 13 sheets defined
      25.5% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1346 through 1355
    Processing helix  chain 'A' and resid 1404 through 1409
    Processing helix  chain 'A' and resid 1424 through 1429
    Processing helix  chain 'A' and resid 1431 through 1441
      removed outlier: 4.327A  pdb=" N   LEU A1435 " --> pdb=" O   MET A1431 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   PHE A1436 " --> pdb=" O   LYS A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1465 through 1469
    Processing helix  chain 'A' and resid 1496 through 1509
      removed outlier: 3.917A  pdb=" N   LEU A1500 " --> pdb=" O   ALA A1496 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   LYS A1502 " --> pdb=" O   ALA A1498 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE A1505 " --> pdb=" O   ARG A1501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1516
      removed outlier: 3.683A  pdb=" N   ASP A1515 " --> pdb=" O   LYS A1512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1528 through 1537
      removed outlier: 3.631A  pdb=" N   LYS A1532 " --> pdb=" O   VAL A1528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1540
      No H-bonds generated for 'chain 'A' and resid 1538 through 1540'
    Processing helix  chain 'A' and resid 1549 through 1561
      removed outlier: 3.775A  pdb=" N   GLU A1559 " --> pdb=" O   GLN A1555 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASN A1560 " --> pdb=" O   LEU A1556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1573 through 1578
      removed outlier: 3.650A  pdb=" N   ASN A1577 " --> pdb=" O   VAL A1573 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU A1578 " --> pdb=" O   HIS A1574 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1573 through 1578'
    Processing helix  chain 'A' and resid 1599 through 1607
      removed outlier: 3.513A  pdb=" N   LEU A1603 " --> pdb=" O   GLU A1599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1608 through 1613
    Processing helix  chain 'A' and resid 1703 through 1715
      removed outlier: 5.723A  pdb=" N   ILE A1709 " --> pdb=" O   TRP A1705 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASN A1710 " --> pdb=" O   SER A1706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1773 through 1785
      removed outlier: 4.019A  pdb=" N   LEU A1777 " --> pdb=" O   GLY A1773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1796
      removed outlier: 4.001A  pdb=" N   LEU A1795 " --> pdb=" O   PHE A1792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1856 through 1861
      removed outlier: 4.347A  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 1921
    Processing helix  chain 'A' and resid 1955 through 1961
      removed outlier: 3.864A  pdb=" N   GLN A1961 " --> pdb=" O   ARG A1957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1967 through 1988
    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: 3.528A  pdb=" N   SER A2058 " --> pdb=" O   ALA A2054 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A2062 " --> pdb=" O   SER A2058 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2071 through 2079
      removed outlier: 3.566A  pdb=" N   GLU A2075 " --> pdb=" O   GLY A2071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2094 through 2100
    Processing helix  chain 'A' and resid 2107 through 2114
    Processing helix  chain 'A' and resid 2124 through 2134
      removed outlier: 3.746A  pdb=" N   PHE A2129 " --> pdb=" O   SER A2125 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ASP A2130 " --> pdb=" O   ALA A2126 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER A2134 " --> pdb=" O   ASP A2130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2135 through 2140
      removed outlier: 3.733A  pdb=" N   CYS A2139 " --> pdb=" O   ALA A2135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2278 through 2282
      removed outlier: 4.012A  pdb=" N   LYS A2281 " --> pdb=" O   LYS A2278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2337 through 2344
      removed outlier: 3.865A  pdb=" N   THR A2340 " --> pdb=" O   GLU A2337 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A2341 " --> pdb=" O   THR A2338 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   GLN A2342 " --> pdb=" O   ARG A2339 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU A2343 " --> pdb=" O   THR A2340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2346 through 2351
      removed outlier: 3.621A  pdb=" N   SER A2350 " --> pdb=" O   TYR A2346 " (cutoff:3.500A)
      removed outlier: 3.683A  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 2396
      removed outlier: 3.560A  pdb=" N   GLU A2395 " --> pdb=" O   HIS A2391 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   VAL A2396 " --> pdb=" O   PHE A2392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2504 through 2513
      removed outlier: 3.604A  pdb=" N   HIS A2510 " --> pdb=" O   ASN A2506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2514 through 2521
      removed outlier: 3.848A  pdb=" N   ALA A2518 " --> pdb=" O   ARG A2514 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1415 through 1419
      removed outlier: 6.244A  pdb=" N   TYR A1415 " --> pdb=" O   ILE A1448 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   VAL A1450 " --> pdb=" O   TYR A1415 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ALA A1417 " --> pdb=" O   VAL A1450 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1547 through 1548
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1690 through 1693
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1696 through 1697
      removed outlier: 3.715A  pdb=" N   MET A1697 " --> pdb=" O   SER A1761 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1884 through 1886
      removed outlier: 6.814A  pdb=" N   VAL A1893 " --> pdb=" O   LEU A1885 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   MET A1944 " --> pdb=" O   GLY A1939 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLY A1939 " --> pdb=" O   MET A1944 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   GLU A1948 " --> pdb=" O   LEU A1935 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   LEU A1935 " --> pdb=" O   GLU A1948 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1953 through 1954
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2142 through 2145
      removed outlier: 6.835A  pdb=" N   VAL A2469 " --> pdb=" O   THR A2460 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   THR A2460 " --> pdb=" O   VAL A2469 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU A2471 " --> pdb=" O   MET A2458 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET A2458 " --> pdb=" O   LEU A2471 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU A2473 " --> pdb=" O   ARG A2456 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 2155 through 2157
      removed outlier: 7.010A  pdb=" N   GLY A2177 " --> pdb=" O   VAL A2194 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY A2188 " --> pdb=" O   ASP A2183 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 2199 through 2207
      removed outlier: 6.681A  pdb=" N   GLY A2218 " --> pdb=" O   LEU A2200 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   LEU A2202 " --> pdb=" O   VAL A2216 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL A2216 " --> pdb=" O   LEU A2202 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   LEU A2204 " --> pdb=" O   TRP A2214 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   TRP A2214 " --> pdb=" O   LEU A2204 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   HIS A2206 " --> pdb=" O   GLU A2212 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLU A2212 " --> pdb=" O   HIS A2206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 2245 through 2249
      removed outlier: 6.692A  pdb=" N   GLY A2266 " --> pdb=" O   THR A2246 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   LEU A2248 " --> pdb=" O   LEU A2264 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU A2264 " --> pdb=" O   LEU A2248 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR A2267 " --> pdb=" O   LYS A2271 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   LYS A2271 " --> pdb=" O   THR A2267 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 2300 through 2305
      removed outlier: 4.089A  pdb=" N   CYS A2302 " --> pdb=" O   GLY A2318 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ILE A2323 " --> pdb=" O   ILE A2336 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   SER A2325 " --> pdb=" O   LYS A2334 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   LYS A2334 " --> pdb=" O   SER A2325 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 2354 through 2358
      removed outlier: 6.809A  pdb=" N   ALA A2366 " --> pdb=" O   ILE A2355 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   VAL A2357 " --> pdb=" O   TYR A2364 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TYR A2364 " --> pdb=" O   VAL A2357 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU A2374 " --> pdb=" O   ILE A2365 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   LYS A2367 " --> pdb=" O   VAL A2372 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   VAL A2372 " --> pdb=" O   LYS A2367 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLY A2385 " --> pdb=" O   VAL A2375 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ASP A2377 " --> pdb=" O   LEU A2383 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU A2383 " --> pdb=" O   ASP A2377 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 2417 through 2420
      removed outlier: 6.651A  pdb=" N   ILE A2434 " --> pdb=" O   VAL A2447 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   VAL A2447 " --> pdb=" O   ILE A2434 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LEU A2436 " --> pdb=" O   ILE A2445 " (cutoff:3.500A)

    216 hydrogen bonds defined for protein.
    585 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: 1.36

  Time building geometry restraints manager: 0.66 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: 2788
        1.34 -     1.46: 1787
        1.46 -     1.58: 4111
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8764
  Sorted by residual:
  bond pdb=" CA  ASN A1867 "
       pdb=" C   ASN A1867 "
    ideal  model  delta    sigma   weight residual
    1.522  1.571 -0.049 1.72e-02 3.38e+03 8.17e+00
  bond pdb=" CB  GLU A1681 "
       pdb=" CG  GLU A1681 "
    ideal  model  delta    sigma   weight residual
    1.520  1.580 -0.060 3.00e-02 1.11e+03 3.97e+00
  bond pdb=" CG1 ILE A1784 "
       pdb=" CD1 ILE A1784 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.66e+00
  bond pdb=" CA  GLU A1681 "
       pdb=" CB  GLU A1681 "
    ideal  model  delta    sigma   weight residual
    1.533  1.554 -0.021 1.37e-02 5.33e+03 2.27e+00
  bond pdb=" N   LYS A2211 "
       pdb=" CA  LYS A2211 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.29e-02 6.01e+03 2.07e+00
  ... (remaining 8759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 11585
        2.72 -     5.45: 248
        5.45 -     8.17: 49
        8.17 -    10.89: 5
       10.89 -    13.62: 1
  Bond angle restraints: 11888
  Sorted by residual:
  angle pdb=" N   ILE A2020 "
        pdb=" CA  ILE A2020 "
        pdb=" C   ILE A2020 "
      ideal   model   delta    sigma   weight residual
     113.71  107.14    6.57 9.50e-01 1.11e+00 4.79e+01
  angle pdb=" C   SER A1366 "
        pdb=" CA  SER A1366 "
        pdb=" CB  SER A1366 "
      ideal   model   delta    sigma   weight residual
     116.54  110.24    6.30 1.15e+00 7.56e-01 3.00e+01
  angle pdb=" CB  LYS A2382 "
        pdb=" CG  LYS A2382 "
        pdb=" CD  LYS A2382 "
      ideal   model   delta    sigma   weight residual
     111.30  120.79   -9.49 2.30e+00 1.89e-01 1.70e+01
  angle pdb=" C   PHE A1650 "
        pdb=" N   LYS A1651 "
        pdb=" CA  LYS A1651 "
      ideal   model   delta    sigma   weight residual
     122.07  129.10   -7.03 1.71e+00 3.42e-01 1.69e+01
  angle pdb=" CA  LEU A1749 "
        pdb=" CB  LEU A1749 "
        pdb=" CG  LEU A1749 "
      ideal   model   delta    sigma   weight residual
     116.30  129.92  -13.62 3.50e+00 8.16e-02 1.51e+01
  ... (remaining 11883 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.55: 5083
       28.55 -    57.10: 186
       57.10 -    85.65: 16
       85.65 -   114.20: 6
      114.20 -   142.75: 1
  Dihedral angle restraints: 5292
    sinusoidal: 2034
      harmonic: 3258
  Sorted by residual:
  dihedral pdb=" CA  TYR A1649 "
           pdb=" C   TYR A1649 "
           pdb=" N   PHE A1650 "
           pdb=" CA  PHE A1650 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.39  -38.61     0      5.00e+00 4.00e-02 5.96e+01
  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  148.74   31.26     0      5.00e+00 4.00e-02 3.91e+01
  dihedral pdb=" CA  PHE A1650 "
           pdb=" C   PHE A1650 "
           pdb=" N   LYS A1651 "
           pdb=" CA  LYS A1651 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.99   30.01     0      5.00e+00 4.00e-02 3.60e+01
  ... (remaining 5289 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1012
       0.053 -    0.106: 316
       0.106 -    0.159: 63
       0.159 -    0.212: 7
       0.212 -    0.266: 1
  Chirality restraints: 1399
  Sorted by residual:
  chirality pdb=" CB  VAL A2513 "
            pdb=" CA  VAL A2513 "
            pdb=" CG1 VAL A2513 "
            pdb=" CG2 VAL A2513 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  ARG A1993 "
            pdb=" N   ARG A1993 "
            pdb=" C   ARG A1993 "
            pdb=" CB  ARG A1993 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CA  ASN A1489 "
            pdb=" N   ASN A1489 "
            pdb=" C   ASN A1489 "
            pdb=" CB  ASN A1489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.78e-01
  ... (remaining 1396 not shown)

  Planarity restraints: 1494
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1587 "    0.069 5.00e-02 4.00e+02   1.05e-01 1.77e+01
        pdb=" N   PRO A1588 "   -0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A1588 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A1588 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A1681 "   -0.020 2.00e-02 2.50e+03   4.07e-02 1.65e+01
        pdb=" CD  GLU A1681 "    0.070 2.00e-02 2.50e+03
        pdb=" OE1 GLU A1681 "   -0.025 2.00e-02 2.50e+03
        pdb=" OE2 GLU A1681 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A1405 "   -0.052 5.00e-02 4.00e+02   7.73e-02 9.57e+00
        pdb=" N   PRO A1406 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A1406 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A1406 "   -0.043 5.00e-02 4.00e+02
  ... (remaining 1491 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 261
        2.70 -     3.25: 8418
        3.25 -     3.80: 13170
        3.80 -     4.35: 16941
        4.35 -     4.90: 27336
  Nonbonded interactions: 66126
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A2246 "
            pdb=" O   LEU A2300 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" O   THR A2321 "
            pdb=" OG1 THR A2338 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   MET A1697 "
            pdb=" OG  SER A1761 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" NE1 TRP A2104 "
            pdb=" O   LEU A2137 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG1 THR A2141 "
            pdb=" O   VAL A2495 "
     model   vdw
     2.289 3.040
  ... (remaining 66121 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     8.700
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5190
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8764  Z= 0.185
  Angle     :  0.975  13.616  11888  Z= 0.503
  Chirality :  0.052   0.266   1399
  Planarity :  0.007   0.105   1494
  Dihedral  : 14.924 142.749   3174
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 11.22 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.67 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.00 %
    Twisted General : 0.19 %

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: -2.92 (0.24), residues: 1096
  helix: -1.95 (0.30), residues: 257
  sheet: -0.62 (0.38), residues: 185
  loop : -2.43 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A2456 
 TYR   0.020   0.002   TYR A2057 
 PHE   0.018   0.002   PHE A1487 
 TRP   0.034   0.003   TRP A1602 
 HIS   0.016   0.002   HIS A1783 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.18 ( 8764)
  covalent geometry    : angle       0.97511 /  0.50 (11888)
  hydrogen bonds       : bond        0.18046 / 12.45 (  216)
  hydrogen bonds       : angle       7.75712 /  5.80 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1448 ILE cc_start: 0.6449 (tp) cc_final: 0.6165 (mp)
REVERT: A 1449 LEU cc_start: 0.7335 (tp) cc_final: 0.7074 (tp)
REVERT: A 1466 MET cc_start: 0.7286 (mmt) cc_final: 0.6602 (mmt)
REVERT: A 1479 PHE cc_start: 0.4269 (m-80) cc_final: 0.3425 (m-80)
REVERT: A 1499 LYS cc_start: 0.5728 (tptt) cc_final: 0.5520 (pttp)
REVERT: A 1605 LYS cc_start: 0.8490 (mttt) cc_final: 0.8266 (mttt)
REVERT: A 1681 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6682 (mt-10)
REVERT: A 1698 PRO cc_start: 0.8168 (Cg_exo) cc_final: 0.7451 (Cg_endo)
REVERT: A 1702 MET cc_start: 0.1194 (tpt) cc_final: 0.0671 (tpt)
REVERT: A 1716 SER cc_start: 0.7808 (t) cc_final: 0.7406 (m)
REVERT: A 1733 TYR cc_start: 0.7035 (m-80) cc_final: 0.6534 (m-80)
REVERT: A 1796 LEU cc_start: 0.4824 (mm) cc_final: 0.4056 (pp)
REVERT: A 1829 ASP cc_start: 0.5695 (m-30) cc_final: 0.5418 (p0)
REVERT: A 1952 LYS cc_start: 0.7393 (tppt) cc_final: 0.7090 (mmtm)
REVERT: A 2099 TYR cc_start: 0.5076 (m-80) cc_final: 0.4734 (m-10)
REVERT: A 2214 TRP cc_start: 0.6684 (m100) cc_final: 0.5746 (m100)
REVERT: A 2241 MET cc_start: -0.2528 (tpt) cc_final: -0.3166 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1019
  time to fit residues: 29.4324
Evaluate side-chains
  129 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106]
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0170
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0270
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.0080

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1730 ASN
** A1783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1926 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1928 HIS
** A1972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.210887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.167730 restraints weight = 35959.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.174981 restraints weight = 19340.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.178089 restraints weight = 11638.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.179180 restraints weight = 8451.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.179966 restraints weight = 6517.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4549
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4549 r_free = 0.4549    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4549 r_free = 0.4549    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.4549
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5799
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8764  Z= 0.166
  Angle     :  0.803  11.468  11888  Z= 0.404
  Chirality :  0.048   0.221   1399
  Planarity :  0.006   0.082   1494
  Dihedral  :  7.340 142.390   1208
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 11.04 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 10.37 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -2.63 (0.24), residues: 1096
  helix: -1.36 (0.32), residues: 249
  sheet: -0.67 (0.37), residues: 193
  loop : -2.34 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1771 
 TYR   0.011   0.002   TYR A2057 
 PHE   0.016   0.002   PHE A2059 
 TRP   0.027   0.002   TRP A1734 
 HIS   0.008   0.001   HIS A1926 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.17 ( 8764)
  covalent geometry    : angle       0.80291 /  0.40 (11888)
  hydrogen bonds       : bond        0.04351 /  3.00 (  216)
  hydrogen bonds       : angle       5.95335 /  4.28 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1449 LEU cc_start: 0.7365 (tp) cc_final: 0.7072 (tp)
REVERT: A 1479 PHE cc_start: 0.4536 (m-80) cc_final: 0.3336 (m-80)
REVERT: A 1595 LEU cc_start: 0.6013 (mt) cc_final: 0.5750 (pt)
REVERT: A 1607 MET cc_start: 0.7612 (tmm) cc_final: 0.7411 (tmm)
REVERT: A 1771 ARG cc_start: 0.5686 (tpt90) cc_final: 0.4748 (mmm160)
REVERT: A 1952 LYS cc_start: 0.7663 (tppt) cc_final: 0.7424 (mmtm)
REVERT: A 1995 LEU cc_start: 0.5446 (tp) cc_final: 0.4716 (mp)
REVERT: A 2053 GLN cc_start: 0.7313 (tm-30) cc_final: 0.7097 (tm-30)
REVERT: A 2061 LEU cc_start: 0.8021 (mp) cc_final: 0.7764 (mp)
REVERT: A 2168 TRP cc_start: 0.6566 (m100) cc_final: 0.6137 (m100)
REVERT: A 2241 MET cc_start: -0.0816 (tpt) cc_final: -0.2369 (mtm)
REVERT: A 2459 MET cc_start: 0.4601 (ppp) cc_final: 0.3447 (mtt)
  outliers start: 12
  outliers final: 8
  residues processed: 141
  average time/residue: 0.0886
  time to fit residues: 17.4821
Evaluate side-chains
  116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1354 LEU
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1627 SER
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2476 ASN
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [102, 16, 33, 42, 54, 15, 94, 50, 88, 0, 93]
   chunk 102 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 54 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    0.9560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1486 HIS
** A1926 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.208349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.167497 restraints weight = 45416.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.172626 restraints weight = 20771.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.175070 restraints weight = 12573.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.176200 restraints weight = 9050.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.177106 restraints weight = 8726.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.4525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4525 r_free = 0.4525    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4523 r_free = 0.4523    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (7 function evaluations)
r_final: 0.4523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5845
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8764  Z= 0.150
  Angle     :  0.746  10.813  11888  Z= 0.379
  Chirality :  0.047   0.213   1399
  Planarity :  0.005   0.068   1494
  Dihedral  :  7.211 142.674   1208
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.76 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.27 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.25), residues: 1096
  helix: -1.17 (0.33), residues: 250
  sheet: -0.72 (0.38), residues: 190
  loop : -2.27 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1973 
 TYR   0.012   0.002   TYR A2064 
 PHE   0.012   0.002   PHE A1700 
 TRP   0.020   0.002   TRP A1734 
 HIS   0.006   0.001   HIS A1926 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 8764)
  covalent geometry    : angle       0.74589 /  0.38 (11888)
  hydrogen bonds       : bond        0.04019 /  2.72 (  216)
  hydrogen bonds       : angle       5.78332 /  4.16 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A 1449 LEU cc_start: 0.7610 (tp) cc_final: 0.7248 (tp)
REVERT: A 1607 MET cc_start: 0.7147 (tmm) cc_final: 0.6807 (tmm)
REVERT: A 1995 LEU cc_start: 0.5674 (tp) cc_final: 0.4730 (mt)
REVERT: A 2023 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.6145 (m-80)
REVERT: A 2061 LEU cc_start: 0.8138 (mp) cc_final: 0.7938 (mp)
REVERT: A 2241 MET cc_start: -0.1895 (tpt) cc_final: -0.2931 (mtm)
REVERT: A 2459 MET cc_start: 0.5234 (ppp) cc_final: 0.3751 (mtt)
  outliers start: 15
  outliers final: 10
  residues processed: 130
  average time/residue: 0.0828
  time to fit residues: 15.4542
Evaluate side-chains
  118 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1977 HIS
Chi-restraints excluded: chain A residue 2004 THR
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2023 TYR
Chi-restraints excluded: chain A residue 2141 THR
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [45, 31, 72, 80, 39, 24, 86, 4, 49, 21, 96]
   chunk 45 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0020
   chunk 80 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 86 optimal weight:   30.0000
   chunk 4 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   overall best weight:    0.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1926 HIS
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A2052 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.210417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.165462 restraints weight = 37917.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.173190 restraints weight = 19079.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.176485 restraints weight = 11433.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.177914 restraints weight = 8581.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.179255 restraints weight = 6377.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4534 r_free = 0.4534    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4535 r_free = 0.4535    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (4 function evaluations)
r_final: 0.4535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8764  Z= 0.127
  Angle     :  0.720  13.134  11888  Z= 0.362
  Chirality :  0.046   0.219   1399
  Planarity :  0.005   0.061   1494
  Dihedral  :  7.029 142.617   1208
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.13 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 16.61 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.25), residues: 1096
  helix: -1.08 (0.33), residues: 247
  sheet: -0.64 (0.38), residues: 184
  loop : -2.21 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1973 
 TYR   0.011   0.001   TYR A2064 
 PHE   0.011   0.001   PHE A1597 
 TRP   0.016   0.002   TRP A1742 
 HIS   0.006   0.001   HIS A1926 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 8764)
  covalent geometry    : angle       0.72008 /  0.36 (11888)
  hydrogen bonds       : bond        0.03746 /  2.56 (  216)
  hydrogen bonds       : angle       5.66160 /  4.06 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A 1449 LEU cc_start: 0.7565 (tp) cc_final: 0.7225 (tp)
REVERT: A 1477 ARG cc_start: 0.5986 (tpt170) cc_final: 0.4940 (ttt180)
REVERT: A 1479 PHE cc_start: 0.5657 (m-80) cc_final: 0.5401 (m-80)
REVERT: A 1607 MET cc_start: 0.7383 (tmm) cc_final: 0.7028 (tmm)
REVERT: A 1715 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.5806 (mm)
REVERT: A 1987 SER cc_start: 0.7305 (m) cc_final: 0.6944 (p)
REVERT: A 2168 TRP cc_start: 0.6815 (m100) cc_final: 0.6352 (m100)
REVERT: A 2241 MET cc_start: -0.0872 (tpt) cc_final: -0.2286 (mtm)
REVERT: A 2459 MET cc_start: 0.4461 (ppp) cc_final: 0.3372 (mtt)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 0.0815
  time to fit residues: 15.4841
Evaluate side-chains
  125 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1697 MET
Chi-restraints excluded: chain A residue 1715 ILE
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 2004 THR
Chi-restraints excluded: chain A residue 2062 LEU
Chi-restraints excluded: chain A residue 2141 THR
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [31, 84, 19, 52, 87, 3, 54, 25, 66, 22, 74]
   chunk 31 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0970
   chunk 25 optimal weight:    0.3980
   chunk 66 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0470
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.3476

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1425 GLN
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1972 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 = 0.4883 r_free = 0.4883 target = 0.211469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.171534 restraints weight = 50687.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.176938 restraints weight = 23510.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.179460 restraints weight = 14005.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.179991 restraints weight = 9729.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.182140 restraints weight = 9319.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4542 r_free = 0.4542    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4541 r_free = 0.4541    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (9 function evaluations)
r_final: 0.4541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5790
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8764  Z= 0.118
  Angle     :  0.704  13.666  11888  Z= 0.352
  Chirality :  0.045   0.224   1399
  Planarity :  0.005   0.056   1494
  Dihedral  :  6.906 142.467   1208
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  : 10.86 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.50 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.32 (0.25), residues: 1096
  helix: -0.91 (0.34), residues: 241
  sheet: -0.55 (0.38), residues: 184
  loop : -2.18 (0.23), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1771 
 TYR   0.013   0.001   TYR A1992 
 PHE   0.013   0.001   PHE A2059 
 TRP   0.013   0.001   TRP A1734 
 HIS   0.005   0.001   HIS A1972 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 8764)
  covalent geometry    : angle       0.70405 /  0.35 (11888)
  hydrogen bonds       : bond        0.03599 /  2.44 (  216)
  hydrogen bonds       : angle       5.60150 /  4.00 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A 1449 LEU cc_start: 0.7529 (tp) cc_final: 0.7201 (tp)
REVERT: A 1479 PHE cc_start: 0.5462 (m-80) cc_final: 0.5223 (m-80)
REVERT: A 1607 MET cc_start: 0.7310 (tmm) cc_final: 0.6921 (tmm)
REVERT: A 1649 TYR cc_start: 0.7046 (t80) cc_final: 0.6822 (t80)
REVERT: A 1971 GLN cc_start: 0.7711 (tm-30) cc_final: 0.6954 (mt0)
REVERT: A 1987 SER cc_start: 0.7140 (m) cc_final: 0.6763 (p)
REVERT: A 1995 LEU cc_start: 0.4828 (tp) cc_final: 0.3812 (mt)
REVERT: A 2061 LEU cc_start: 0.8255 (mp) cc_final: 0.7457 (tt)
REVERT: A 2066 ILE cc_start: 0.8797 (pt) cc_final: 0.8585 (pt)
REVERT: A 2168 TRP cc_start: 0.6416 (m100) cc_final: 0.6137 (m100)
REVERT: A 2241 MET cc_start: -0.1600 (tpt) cc_final: -0.3005 (mtt)
REVERT: A 2459 MET cc_start: 0.4977 (ppp) cc_final: 0.3615 (mtt)
  outliers start: 14
  outliers final: 10
  residues processed: 127
  average time/residue: 0.0855
  time to fit residues: 15.5833
Evaluate side-chains
  117 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1343 THR
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1697 MET
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2141 THR
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [94, 56, 73, 26, 71, 13, 35, 40, 102, 96, 20]
   chunk 94 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   chunk 73 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0570
   chunk 71 optimal weight:    0.0040
   chunk 13 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    0.0040
   chunk 102 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.0532

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1972 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.217881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.184514 restraints weight = 35677.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.188333 restraints weight = 21457.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.189939 restraints weight = 14918.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.191379 restraints weight = 10782.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.192040 restraints weight = 10093.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4609 r_free = 0.4609    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4609 r_free = 0.4609    target_work(ls_wunit_k1) = 0.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5651
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8764  Z= 0.115
  Angle     :  0.700  16.394  11888  Z= 0.348
  Chirality :  0.045   0.226   1399
  Planarity :  0.004   0.053   1494
  Dihedral  :  6.801 142.248   1208
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.49 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.17 %
    Favored  : 81.16 %
  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: -2.13 (0.25), residues: 1096
  helix: -0.67 (0.35), residues: 238
  sheet: -0.34 (0.39), residues: 182
  loop : -2.12 (0.23), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1771 
 TYR   0.028   0.001   TYR A1747 
 PHE   0.018   0.001   PHE A2083 
 TRP   0.014   0.001   TRP A2214 
 HIS   0.004   0.001   HIS A1972 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 ( 8764)
  covalent geometry    : angle       0.70029 /  0.35 (11888)
  hydrogen bonds       : bond        0.03383 /  2.28 (  216)
  hydrogen bonds       : angle       5.48397 /  3.93 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A 1425 GLN cc_start: 0.6528 (mm-40) cc_final: 0.6179 (mm-40)
REVERT: A 1449 LEU cc_start: 0.7312 (tp) cc_final: 0.7010 (tp)
REVERT: A 1607 MET cc_start: 0.7063 (tmm) cc_final: 0.6617 (tmm)
REVERT: A 1649 TYR cc_start: 0.6900 (t80) cc_final: 0.6593 (t80)
REVERT: A 1702 MET cc_start: 0.2587 (mmm) cc_final: 0.0583 (mmt)
REVERT: A 1735 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5040 (ptp-170)
REVERT: A 1971 GLN cc_start: 0.7575 (tm-30) cc_final: 0.6908 (mt0)
REVERT: A 1987 SER cc_start: 0.7393 (m) cc_final: 0.7047 (p)
REVERT: A 2061 LEU cc_start: 0.8016 (mp) cc_final: 0.7334 (tt)
REVERT: A 2168 TRP cc_start: 0.6026 (m100) cc_final: 0.5764 (m100)
REVERT: A 2241 MET cc_start: -0.1948 (tpt) cc_final: -0.3134 (mtt)
REVERT: A 2459 MET cc_start: 0.5155 (ppp) cc_final: 0.3913 (mtt)
  outliers start: 13
  outliers final: 8
  residues processed: 132
  average time/residue: 0.0841
  time to fit residues: 15.9870
Evaluate side-chains
  118 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1735 ARG
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1977 HIS
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [29, 63, 44, 19, 79, 61, 109, 108, 104, 33, 59]
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   chunk 104 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0770
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6540

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.214335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.178087 restraints weight = 51599.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.181352 restraints weight = 27144.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.184145 restraints weight = 17461.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.184840 restraints weight = 12382.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.186152 restraints weight = 11454.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4517 r_free = 0.4517    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4518 r_free = 0.4518    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5816
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8764  Z= 0.126
  Angle     :  0.719  16.044  11888  Z= 0.356
  Chirality :  0.045   0.216   1399
  Planarity :  0.005   0.050   1494
  Dihedral  :  6.831 142.350   1208
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.40 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.17 %
    Favored  : 80.94 %
  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: -2.11 (0.25), residues: 1096
  helix: -0.62 (0.35), residues: 236
  sheet: -0.54 (0.38), residues: 192
  loop : -2.05 (0.24), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1771 
 TYR   0.016   0.001   TYR A1747 
 PHE   0.009   0.001   PHE A2083 
 TRP   0.012   0.001   TRP A2496 
 HIS   0.004   0.001   HIS A2510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 8764)
  covalent geometry    : angle       0.71903 /  0.36 (11888)
  hydrogen bonds       : bond        0.03600 /  2.44 (  216)
  hydrogen bonds       : angle       5.50417 /  3.90 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A 1425 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6234 (mm-40)
REVERT: A 1449 LEU cc_start: 0.7528 (tp) cc_final: 0.7208 (tp)
REVERT: A 1607 MET cc_start: 0.7066 (tmm) cc_final: 0.6704 (tmm)
REVERT: A 1649 TYR cc_start: 0.6938 (t80) cc_final: 0.6632 (t80)
REVERT: A 1715 ILE cc_start: 0.6088 (OUTLIER) cc_final: 0.5455 (mm)
REVERT: A 1971 GLN cc_start: 0.7691 (tm-30) cc_final: 0.6974 (mt0)
REVERT: A 1987 SER cc_start: 0.7387 (m) cc_final: 0.7074 (p)
REVERT: A 1995 LEU cc_start: 0.5650 (tp) cc_final: 0.4632 (mt)
REVERT: A 2061 LEU cc_start: 0.8314 (mp) cc_final: 0.7584 (tt)
REVERT: A 2064 TYR cc_start: 0.6084 (t80) cc_final: 0.5816 (t80)
REVERT: A 2241 MET cc_start: -0.1774 (tpt) cc_final: -0.3034 (mtt)
REVERT: A 2301 MET cc_start: 0.3963 (mpp) cc_final: 0.2905 (ptp)
REVERT: A 2459 MET cc_start: 0.5270 (ppp) cc_final: 0.3848 (mtt)
  outliers start: 15
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0740
  time to fit residues: 13.1769
Evaluate side-chains
  120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1354 LEU
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1715 ILE
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1776 LEU
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1977 HIS
Chi-restraints excluded: chain A residue 1991 ILE
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2024 CYS
Chi-restraints excluded: chain A residue 2068 THR
Chi-restraints excluded: chain A residue 2504 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [60, 85, 65, 23, 73, 43, 2, 25, 84, 89, 57]
   chunk 60 optimal weight:    1.9990
   chunk 85 optimal weight:   40.0000
   chunk 65 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0030
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.206912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.159092 restraints weight = 48333.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.168077 restraints weight = 22073.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.168740 restraints weight = 12351.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.170721 restraints weight = 9647.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.172037 restraints weight = 7914.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.4423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4422 r_free = 0.4422    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.4422
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6070
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8764  Z= 0.150
  Angle     :  0.747  16.123  11888  Z= 0.370
  Chirality :  0.046   0.197   1399
  Planarity :  0.005   0.049   1494
  Dihedral  :  7.012 142.509   1208
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.87 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.73 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.26), residues: 1096
  helix: -0.74 (0.34), residues: 250
  sheet: -0.45 (0.38), residues: 197
  loop : -2.02 (0.24), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1973 
 TYR   0.016   0.002   TYR A1699 
 PHE   0.011   0.001   PHE A1700 
 TRP   0.014   0.002   TRP A2496 
 HIS   0.006   0.001   HIS A2510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 8764)
  covalent geometry    : angle       0.74678 /  0.37 (11888)
  hydrogen bonds       : bond        0.03841 /  2.65 (  216)
  hydrogen bonds       : angle       5.63831 /  3.98 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A 1425 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6323 (mm-40)
REVERT: A 1427 GLU cc_start: 0.7109 (pt0) cc_final: 0.5984 (mm-30)
REVERT: A 1607 MET cc_start: 0.7464 (tmm) cc_final: 0.7041 (tmm)
REVERT: A 1649 TYR cc_start: 0.7114 (t80) cc_final: 0.6740 (t80)
REVERT: A 1715 ILE cc_start: 0.6329 (OUTLIER) cc_final: 0.5670 (mm)
REVERT: A 1971 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7030 (mt0)
REVERT: A 1987 SER cc_start: 0.7533 (m) cc_final: 0.7145 (p)
REVERT: A 2061 LEU cc_start: 0.8337 (mp) cc_final: 0.7488 (tt)
REVERT: A 2241 MET cc_start: -0.0431 (tpt) cc_final: -0.2174 (mtt)
REVERT: A 2301 MET cc_start: 0.3515 (mpp) cc_final: 0.3213 (ptp)
REVERT: A 2459 MET cc_start: 0.4437 (ppp) cc_final: 0.3320 (mtt)
  outliers start: 15
  outliers final: 11
  residues processed: 122
  average time/residue: 0.0814
  time to fit residues: 14.6097
Evaluate side-chains
  114 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1354 LEU
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1697 MET
Chi-restraints excluded: chain A residue 1715 ILE
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1991 ILE
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2068 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [69, 26, 52, 95, 11, 34, 35, 92, 88, 59, 4]
   chunk 69 optimal weight:    0.6980
   chunk 26 optimal weight:    0.3980
   chunk 52 optimal weight:    7.9990
   chunk 95 optimal weight:    0.3980
   chunk 11 optimal weight:    7.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:   20.0000
   chunk 88 optimal weight:   40.0000
   chunk 59 optimal weight:    0.0970
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4868 r_free = 0.4868 target = 0.208622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.163870 restraints weight = 35572.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.170371 restraints weight = 19833.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.175894 restraints weight = 10623.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.176306 restraints weight = 7322.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.176678 restraints weight = 6028.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4485 r_free = 0.4485    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4484 r_free = 0.4484    target_work(ls_wunit_k1) = 0.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5936
moved from start:          0.5075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8764  Z= 0.124
  Angle     :  0.725  15.528  11888  Z= 0.360
  Chirality :  0.045   0.208   1399
  Planarity :  0.004   0.048   1494
  Dihedral  :  6.915 142.518   1208
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 10.21 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.51 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.25), residues: 1096
  helix: -0.61 (0.35), residues: 246
  sheet: -0.33 (0.39), residues: 186
  loop : -2.08 (0.24), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1771 
 TYR   0.026   0.002   TYR A2449 
 PHE   0.010   0.001   PHE A1597 
 TRP   0.017   0.002   TRP A2426 
 HIS   0.007   0.001   HIS A1911 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 ( 8764)
  covalent geometry    : angle       0.72488 /  0.36 (11888)
  hydrogen bonds       : bond        0.03618 /  2.50 (  216)
  hydrogen bonds       : angle       5.47435 /  3.84 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A 1425 GLN cc_start: 0.6545 (mm-40) cc_final: 0.6142 (mm-40)
REVERT: A 1427 GLU cc_start: 0.7027 (pt0) cc_final: 0.5914 (mm-30)
REVERT: A 1607 MET cc_start: 0.7467 (tmm) cc_final: 0.7213 (tmm)
REVERT: A 1649 TYR cc_start: 0.6854 (t80) cc_final: 0.6548 (t80)
REVERT: A 1971 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7015 (mt0)
REVERT: A 1987 SER cc_start: 0.7601 (m) cc_final: 0.7256 (p)
REVERT: A 2061 LEU cc_start: 0.8154 (mp) cc_final: 0.7371 (tt)
REVERT: A 2241 MET cc_start: -0.1112 (tpt) cc_final: -0.2654 (mtt)
REVERT: A 2301 MET cc_start: 0.3602 (mpp) cc_final: 0.3280 (ptp)
REVERT: A 2459 MET cc_start: 0.4475 (ppp) cc_final: 0.3378 (mtt)
  outliers start: 14
  outliers final: 14
  residues processed: 116
  average time/residue: 0.0760
  time to fit residues: 12.9704
Evaluate side-chains
  117 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1354 LEU
Chi-restraints excluded: chain A residue 1404 THR
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1697 MET
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1928 HIS
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1991 ILE
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2024 CYS
Chi-restraints excluded: chain A residue 2127 GLN
Chi-restraints excluded: chain A residue 2193 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [109, 43, 53, 84, 10, 62, 15, 12, 63, 85, 95]
   chunk 109 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0870
   chunk 53 optimal weight:    0.6980
   chunk 84 optimal weight:   20.0000
   chunk 10 optimal weight:    0.0870
   chunk 62 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0170
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.3374

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.209324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.162618 restraints weight = 59830.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.171946 restraints weight = 22650.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.173436 restraints weight = 12405.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.174493 restraints weight = 9860.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.176128 restraints weight = 8230.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.4471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4473 r_free = 0.4473    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4473 r_free = 0.4473    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5952
moved from start:          0.5178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8764  Z= 0.120
  Angle     :  0.726  15.345  11888  Z= 0.360
  Chirality :  0.045   0.208   1399
  Planarity :  0.004   0.048   1494
  Dihedral  :  6.894 142.385   1208
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.04 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.28 %
    Favored  : 79.93 %
  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: -2.06 (0.25), residues: 1096
  helix: -0.61 (0.35), residues: 247
  sheet: -0.49 (0.38), residues: 192
  loop : -2.03 (0.24), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1771 
 TYR   0.012   0.001   TYR A2099 
 PHE   0.012   0.001   PHE A1511 
 TRP   0.014   0.001   TRP A2426 
 HIS   0.004   0.001   HIS A1911 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 8764)
  covalent geometry    : angle       0.72595 /  0.36 (11888)
  hydrogen bonds       : bond        0.03490 /  2.40 (  216)
  hydrogen bonds       : angle       5.47429 /  3.85 (  585)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A 1425 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6257 (mm-40)
REVERT: A 1427 GLU cc_start: 0.7102 (pt0) cc_final: 0.5926 (mm-30)
REVERT: A 1649 TYR cc_start: 0.6790 (t80) cc_final: 0.6491 (t80)
REVERT: A 1702 MET cc_start: 0.2388 (mmm) cc_final: 0.1139 (mmt)
REVERT: A 1971 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7010 (mt0)
REVERT: A 1987 SER cc_start: 0.7606 (m) cc_final: 0.7242 (p)
REVERT: A 1995 LEU cc_start: 0.5520 (mt) cc_final: 0.4679 (mt)
REVERT: A 2061 LEU cc_start: 0.8292 (mp) cc_final: 0.7518 (tt)
REVERT: A 2064 TYR cc_start: 0.6272 (t80) cc_final: 0.5943 (t80)
REVERT: A 2241 MET cc_start: -0.0789 (tpt) cc_final: -0.2368 (mtt)
REVERT: A 2301 MET cc_start: 0.3596 (mpp) cc_final: 0.3264 (ptp)
REVERT: A 2459 MET cc_start: 0.4453 (ppp) cc_final: 0.3452 (mtt)
  outliers start: 14
  outliers final: 13
  residues processed: 117
  average time/residue: 0.0765
  time to fit residues: 13.2197
Evaluate side-chains
  116 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1354 LEU
Chi-restraints excluded: chain A residue 1357 THR
Chi-restraints excluded: chain A residue 1543 ILE
Chi-restraints excluded: chain A residue 1680 ILE
Chi-restraints excluded: chain A residue 1697 MET
Chi-restraints excluded: chain A residue 1754 VAL
Chi-restraints excluded: chain A residue 1792 PHE
Chi-restraints excluded: chain A residue 1928 HIS
Chi-restraints excluded: chain A residue 1935 LEU
Chi-restraints excluded: chain A residue 1991 ILE
Chi-restraints excluded: chain A residue 2015 ILE
Chi-restraints excluded: chain A residue 2024 CYS
Chi-restraints excluded: chain A residue 2068 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks: [71, 85, 1, 55, 3, 92, 12, 2, 109, 89, 26]
   chunk 71 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 55 optimal weight:    0.3980
   chunk 3 optimal weight:    0.1980
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.206790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.162808 restraints weight = 45949.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.169098 restraints weight = 21524.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.171042 restraints weight = 13539.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.171560 restraints weight = 10541.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.172611 restraints weight = 8977.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4428 r_free = 0.4428    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4428 r_free = 0.4428    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6024
moved from start:          0.5386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8764  Z= 0.139
  Angle     :  0.750  16.020  11888  Z= 0.371
  Chirality :  0.046   0.208   1399
  Planarity :  0.004   0.048   1494
  Dihedral  :  6.991 142.488   1208
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.76 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.39 %
    Favored  : 79.60 %
  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: -2.11 (0.25), residues: 1096
  helix: -0.63 (0.35), residues: 247
  sheet: -0.48 (0.38), residues: 202
  loop : -2.10 (0.24), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1771 
 TYR   0.014   0.002   TYR A2099 
 PHE   0.011   0.001   PHE A1597 
 TRP   0.015   0.001   TRP A2426 
 HIS   0.005   0.001   HIS A2510 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 8764)
  covalent geometry    : angle       0.74994 /  0.37 (11888)
  hydrogen bonds       : bond        0.03732 /  2.58 (  216)
  hydrogen bonds       : angle       5.55130 /  3.88 (  585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1849.63 seconds
wall clock time: 32 minutes 27.38 seconds (1947.38 seconds total)